From 2006.igem.org

Contents 1 Name: Fousion 2 News 3 Organisation 3.1 People 3.1.1 Students 3.1.2 Supervisors 3.2 Timeline 3.3 Tasks 3.4 Parts shopping list

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

Catie Lichten (Center for Nonlinear Dynamics)

Octavio Mondragon (Physics)

Belinda Kong (Microbiology and Immunology)

Adrian Kaats (Biomedical Engineering)

Jamie Schafer (Microbiology and Immunology)

Horia Vulpe (Physiology)

Ashwini Bapat (Biochemistry)

Aaron Lapierre (Anatomy & Cell Biology)

Josh Wright (Chemistry)

Jieun Kim(Biology) Julia Ishak (Biomedical Sciences)

Supervisors

Jay Nadeau

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?

Also try this: BBa_J11002 and BBa_J06913. What happens if you substitute an AAV-degradation-tagged GFP?

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

BBa_J06204: Makes lambda cl protein in response to C4-HSL

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.

BBa_J06910: Lambda induces destabilized (slow LVA) LacI. LacI shuts down EYFP (nondestabilized).

BBa_J06913: If you add 434, you repress lambda (LVA slow destabilized). YFP is downstream of a lambda promoter so by adding 434 you reduce repression and turn on YFP.

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.

BBa_J06917: Lambda induces 434, which represses YFP. not destabilized.

BASIC TOOLS

BBa_I13800: ampicillin resistance

BBa_I13801: kanamycin resistance

SINGLE BLOCKS - TAGS

DEGRADATION TAGS

BBa_M0040 - LVA, slow degradation BBa_M0042 - LAA, medium degradation BBa_M0044 - AAV, fast degradation BBa_M0040 - ASV, fastest degradation

ADHESION TAGS

BBa_M0040: sticks to glutathione BBa_M0021: sticks to zinc, nickel, cobalt

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