From 2006.igem.org

Revision as of 03:30, 30 April 2006

Name: Fousion

News

• 2006-04-14 Discussion page created
• 2006-03-16 First kick-off meeting and team selection

If there is a specific task that we need the bacteria to do (e.g. change colour on cue, aggregate...) list it here. We have a TON of composite bricks, and can plan custom ones. BUT I need to know what U want... I am going nuts looking at the list

Your Dyslexic Dinosaur

Organisation

People

Students

Supervisors

Timeline

• Meetings

Tasks

• Task Assignment

Modelling people: check out these bricks: BBa_I13920, BBa_I13921, BBa_I13922. What happens if you plug these into your computer simulation?

Parts shopping list

Composite bricks - these are the best to use as less cloning is required.

All these bricks express YFP and downregulate it in response to a signal

YELLOW

ARABINOSE RESPONSE.

BBa_E0610: Arabinose turns on lac repressor which in turn shuts down Yellow fluorescent protein.

BBa_E0600: like BBa_E0610 but YFP is destabilized - slow degradation. Not listed as available.

BBa_E0611: Arabinose turns on destabilized TetR repressor which shuts down yellow fluorescent protein. Addition of Tetracyline blocks TetR repressor allowing yellow fluorescent protein to be turned back on.

BBa_E0601: Like BBa_E0611 but YFP is destabilized - slow degradation. Not listed as available

BBa_E0613: Arabinose turns on destabilized lambda repressor which shuts down yellow fluorescent protein.

BBa_E0602: Like BBa_E0613 but YFP is destabilized - slow degradation. Not listed as available

BBa_E0603: Like BBa_E0602 but baseline expression of YFP is higher. Not listed as available

BBa_E0604: Arabinose turns on destabilized 434 cl epressor which in turn shuts down destabilized (slow) Yellow fluorescent protein. Not listed as available

BBa_E0614: Like BBa_E0604 but YFP is not destabilized (hangs around forever). Not listed as available

BBa_E0605: Arabinose turns on destabilized p22 repressor which in turn shuts down destabilized (slow) Yellow fluorescent protein. Not listed as available

BBa_E0615: Like BBa_E0605, but YFP is not destabilized, hangs around forever.

Lac I REGULATED

BBa_I12026: Produces YFP (not destabilized). Controlled by Lac I BBa_I14022: Slow-destabilized (LVA) YFP controlled by Lac promoter

MULTIPLE REGULATORS

BBa_I12051: Lactose induces lambda repressor. Arabinose induces 434 repressor. Lambda repressor activates YFP, 434 represses YFP. YFP is destabilized (AAV, fast).

BBa_I12052: Like BBa_I12051 but promoter for YFP has double binding sites for better control.

LAMBDA regulated

BBa_I13973: Fast destabilized (AAV) YFP controlled by original lambda promoter - lambda protein would repress it.

LAS regulated

BBa_I14013: Slow destabilized YFP under Las promoter.

BBa_I14030: TetR promoter controls LacI repressor, lambda repressor, and YFP. All three are slow (LVA) destabilized.

BASIC COLOR LEGO

BBa_I14005: Slow-destabilized (LVA) YFP with strong ribosome binding site

CYAN

TET response

BBa_I0401: Expresses CFP and lux from the Tet-OFF promoter. Neither is destabilized. Not listed as available

BBa_I0402: Like BBa_I0401 but lux is destabilized (LVA, slow)

BBa_I0404: Produces rhlR and CFP, downregulated by Tet. rhlR binds with N-butyryl-HSL, regulates transcription. rhlR but not CFP is destabilized.

BBa_I0405: same as BBa_I0404, but produces rhIl which produces N-butyryl-HSL.

BBa_I0406: produces CFP and lasR, which accepts chemical signal AI-1. Downregulated by Tet. LasR but not CFP are destabilized.

BBa_I0407. Like BBa_I0406 but produces lasI (destabilized LVA slow) which generates the chemical signal Al-1.

BBa_I0408: produces CFP and CinR, repressed by Tetracycline. Cin R is LVA (slow) destabilized. Cin R binds O3-C14:1-HSL and activates the Cin promoter.

BBa_I0409: Like BBa_I0408 but produces cinL (destabilized LVA slow) which generates the chemical signal O3-C14:1-HSL.

BBa_I14029: LacI promoter controls slow destabilized (LVA) TetR and slow destabilized (LVA) YFP

ARABINOSE response:

BBa_I0403 Expresses CFP and aiiA from an arabinose promoter. aiiA degrades N-acyl homoserine lactones (quorum sensing autoinducers). aiiA but not CFP is destabilized (LVA, slow).

GREEN

ARABINOSE

BBa_I13540: Arabinose turns on green fluorescent protein.

RED:

BBa_I13507: Basic red fluorescent protein: ribosome binding site, red, stop. B.Y.O. promoter.

ARABINOSE

BBa_I13520: Arabinose turns on mRFP. This think was actually shown to work. BBa_I13517: Like BBa_I13520 but weaker ribosome binding site.

SIGNALING

Promoterless (BYOP)

BBa_I0460 aiiA cassette. Produces enzyme which degrades N-acyl homoserine lactones (quorum sensing autoinducers. Destabilized with LVA (slow) B.Y.O.P (Bring your own promoter).

BBa_I10100: Produces adhesin, makes bacteria stick to each other. B.Y.O.P (Bring your own promoter)

BBa_I14002: LVA-destabilized Lac I, with strong ribosome binding site.

BBa_I14003: LVA-destabilized TetR, with strong ribosome binding site.

BBa_I14010: LVA-destabilized Ara C, with strong ribosome binding site.

BBa_I14012: LVA-destabilized LasR, with strong ribosome binding site.

BBa_I14045: LVA-destabilized RhiR, with strong ribosome binding site

BBa_I14046: LVA-destabilized RhiR, with strong ribosome binding site

With promoter

BBa_I14023: Constitutively expresses slow-destabilized LasR protein. BBa_I14023: Constitutively expresses slow-destabilized RhiR protein.

BBa_I12002: Lambda promoter driving expression of 434 repressor. Not destabilized. BBa_I12054: same as BBa_I12002, lambda promoter is modified to be activated by lac repressor cI

BBa_I12055: Hybrid lambda promoter activated by lambda and repressed by 434, driving expression of destablized lambda (LVA slow degradation). This was used as part of an oscillator. BBa_I12056: Like BBa_I12055:but the promoter has duplicate sites for better control.

BBa_I12011: Lambda promoter driving expression of p22 repressor. LVA (slow) destabilized.

BBa_I13271: Cassette: rhiR upstream of rhi promoter. rhiR with butyl-homoserine lactone activates rhi promoter. rhiR needs a promoter, not included. BBa_I13303: Like BBa_I13271 but controlled by lac promoter. BBa_I13309: like BBa_I13303 BBa_I13310: like BBa_I13303 but controlled by TetR BBa_I13312: like BBa_I13303 but controlled by TetR

BBa_I14005, BBa_I14038: RhI promoter upstream of Lac I

BBa_I13305: Lac I induces LasR, LasR with homoserine lactone activates Las promoter (downstream). Can add your own gene after Las promoter.

BBa_I14014: slow destabilized (LVA) LasR under Lac I promoter

BBa_I13016, BBa_S04003: Arabinose induces LVA (slow) destabilized TetR protein.

BBa_I13017, BBa_S04002: Expression of LVA(slow) destabilized TetR protein controlled by lactose (Lac I promoter).

BBa_I14028, BBa_I14036: LVA-destabilized Lambda controlled by LasR promoter.

BBa_I14037: Destabilized LasL controlled by LasR promoter. Lambda operator allows shutdown by lambda repressor.

BBa_I14050: Destabilized RhiL upregulated by Las/HSL and blocked by TetT

CHAIN REACTION PREMADE:

BBa_I13036: Arabinose induces TetR. TetR induces LuxR. LuxR induces YFP if a homoserine lactone signal is received.

BBa_I13037: Lactose induces TetR. TetR induces LuxR. Arabinose induces LuxL which produces homoserine lactone. LuxR and homoserine lactone activate YFP.

BBa_I13038: Arabinose induces TetR, and also luxL which makes homoserine lactone. TetR induces LuxR. LuxL and LuxR together activate YFP.

BBa_I13920: Lux pL makes Lux R protein. Lux R protein + homoserine lactone shuts off Lux pL (no more lux R) and activates Lux pR which makes LacI. Lac I shuts off luxL protein (homoserine lactone) which shuts down lac I and HSL production, Lux pL is free to start over. Lac I and LuxL are slow destabilized, LVA.

BBa_I13921: Same as BBa_I13920 but TetR (LVA destabilized) is substituted for Lac I.

BBa_I13922: Same as BBa_I13920 but lambda repressor (LVA destabilized) is substituted for Lac I.

MOTILITY

TetR control

BBa_I13710: TetR induces CheY, which is a phosphorylation target for motility.

BBa_I13711: TetR induces CheB. CheB can be phosphorylated and will demethylate Aspartate receptors.

BBa_I13712: TetR induces CheR. CheR opposes Che B.

LACTOSE control

BBa_I13721: Lactose induces CheB. (lac promoter)

MULTI-COMPONENT

BBa_I13730: Lac I controls Che B, TetR controls Che R. Che B opposes Che R (chemosensing)

BBa_M30109: light sensor. Activates OmpC and Represses Omp F promoter

BBa_J11002: Generates GFP pulse, slow, not destabilized.

BASIC TOOLS

BBa_I13800: ampicillin resistance

BBa_I13801: kanamycin resistance

=Introduction= Our brainstorming meeting on 3-16 gave us several preliminary ideas which we will explore via modeling and research