Team:Groningen/Brainstorm/Rainbow Bacteria

From 2009.igem.org

Use or mention of the Cre/Lox System

• Tianjin University 2008 (China) – Made use of the CRE/LoxP combination (together with other strategies) to combine DNA and make “Foolproof Plasmid Self-Assembly Systems”.

• MIT 2006 (USA) – Mention of mutant LoxP sites to prevent inversion of sequences (Lox66 and Lox71)

• Imperial College 2006 (London) – Biological oscillator by using the CRE/Lox system as a switch by incorporating DNA to prevent downstream transcription. In the end used Quorum Sensing to create a predator – pray system.

• Paris 2007 (France) – (Synthetic Multicellular Bacterium) Use of CRE/Lox system to influence differentiation in germ line, because it was readily available, largely used and well described. Low concentrations of DAP triggered the transcription of Cre-recombinase (under the influence of DAP-sensitive promoter), which caused the removal of a gene required for bacterial reproduction by site-specific recombination (SSR), and resulted in the activation of a gene for the production of DAP by them. The SSR sites might become a burden.

• Berkeley 2007 (England) – Registration of recombinase parts (Cre), Bacteriophage P1-derived Cre-Lox.

• USTC 2008 (China) – made use of Cre to cut out “sender” genes upon receiving a signal from a sender cell and thereby creating a receiver cell.

• Tsinghua 2008 – use of the Cre/Lox system in their second project, but is unclear why they used it.
• Caltech 2008 - Wilfred Not Cre/LoxP but it does induce variation in the population
• Hong kong 2008 Wilfred Look at the overlapping T7 promoters for variation in response

Use or mention of XFP’s

• Utah State University – use of GFP as a reporter gene to indicate the maximum production level of PHB.

• University of Sheffield – use of GFP as a reporter gene upon detection of a pathogen by a receiver protein.

• UNIPV-Pavia – use of GFP and RFP as reporter genes in electronically based circuit (on/off).

• UCSF – use of GFP as a reporter gene in DNA silencing by Chromatin.

• TUDelft – use of different method to produce colors, but results in this area were not very promising (also due to ordered parts from iGEM).

• Tokyo Tech – use of GFP as a reporter gene in their “coli touch” display experiment.

• Paris – use of (E)CFP, YFP, GFP and mRFP in the construction of a oscillating time clock project.

• Newcastle University – use of a XFP as a reporter gene to indicate the amount of increase in POP’s.

• Missouri University – use of RFP with special introduced promoter.

• Minnesota – use of GFP and RFP as reporter genes.

• Bologna – use of GFP and RFP as reporter genes.

Parts in the [http://partsregistry.org/Main_Page Registry of Standard Parts]:

Fluorescent protein sequences

• Workable are the wild-type GFP (and a few mutants), RFP (and cherry version)
• Not-workable (no info) are YFP and CFP (yellow and cyan), OFP (orange), SBFP2 (blue) and a few mutant proteins.

Recombinase

• Workable are Cre DNA recombinase, and Hin invertase
• No info (not-workable) are mutant (altered stop/start codon) Cre versions, and a few other enzymes like integrase.

Recombination sites

• Workable is the Lox site for recombination
• No info (not-workable) are lox66 and lox71

Membrane proteins

• Only a few mentioned in the lists of receptors, transporters, channels, pumps and “other proteins”, maybe 40 in total, but I am not familiar with these names ([http://en.wikipedia.org/wiki/Toll-like_receptor TLR], Omp).

All of the workable protein sequences are listed as “1 star” in the availability list!!

Literature

• J. Livet et al., Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system, 2007, Nature, Vol. 450, 56-63.
• J. W. Lichtman, J. Livet & J. R. Sanes, A technicolour approach to the connectome, 2008, Nature Reviews neuroscience, Vol. 9, 417-422.