BASIC PARTS
TABLE OF PARTS
OUR PARTS
PART NAME |
PART NUMBER |
FUNCTION |
---|---|---|
MerR + Bidirecional promoter | BBa_K3280005 | MerR regulator protein |
tDGC + rbs | BBa_K3280000 | Biofilm formation |
MBP + linker | BBa_K3280006 | Metal binding peptide |
Wspr | BBa_K3280001 | Biofilm formation |
PREEXISTING PARTS
PART NAME |
PART NUMBER |
FUNCTION |
---|---|---|
YdeH | BBa_K1019004 | Biofilm formation |
YddV | BBa_K748003 | Biofilm formation |
TolC | BBa_K554009 | Part of protein secretion system |
HlyB | BBa_K554007 | Part of protein secretion system |
HlyA | BBa_K554002 | Signal peptide -Part of protein secretion |
HlyD | BBa_K554008 | Part of protein secretion |
BIOFILM FORMATION
YdeH
YdeH is a diguanylate cyclase that is involved in producing the key secondary messenger c-di-GMP. c-di-GMP is proposed to be a "master regulator" of biofilm formation.
Its expression increases surface adhesion and various aspects of the biofilm response.
We use this and others diguanilates (Wspr, YddV) in petSUMO plasmid to run the test. We did experiment with and without agitation, and also testing the efficiency of biofilm in coconut fiber.
In our test YdeH appeared to be very efficient in biofilm production and probably ideal to use in our circuit as YddV.
YddV
Submitted by another iGEM team, iGEM12_HIT-Harbin, (the fragments codes for YddV, a diguanylate cyclase originated from Escherichia coli O7:K1 genome).
We have been running tests of biofilm expression and growth rate of this protein in petSUMO vector intending to add new information about an existing part.
We use this and others diguanilates (Wspr, YdeH) in petSUMO plasmid to run the test. We did experiment with and without agitation, and also testing the efficiency of biofilm in coconut fiber.
In our test YddV appeared to be very efficient in biofilm production and probably ideal to use in our circuit as YdeH.
PA3702 (Wspr)
This part is originated from Pseudomonas aeruginosa. In our project we use this Wspr to test biofilm quantification in order to see what diguanilate is more efficient for our circuit.
We use this and others diguanilates (Yddv and YdeH) in petSUMO plasmid to run the test. We did experiment with and without agitation, and also testing the efficiency of biofilm in coconut fiber.
In our results we conclude that Wspr is the less efficient diguanilate when compared to YdeH and YddV.
MAP
LINEAR
RBS + tDGC
This one is originated from Thermotoga maritima
Cyclic di-GMP (c-di-GMP) is recognized as an intracellular signaling molecule coordinating the “lifestyle transition” from motility to sessility and vice versa (i.e. dispersion).
The correlation between high c-di-GMP concentration in the cell and biofilm formation or between low c-di-GMP levels and motility has been demonstrated in several bacteria species [1].
MAP
LINEAR
MERCURY SYSTEM
MBP (Metal Binding Peptide) + Linker
This part has a segment of BBa_k346004. We added a short linker. MBP is a lead metal-binding peptide engineered from PbrR.
This part is a protein domain and increase levels of c-di-GMP to induce biofilm formation.
MerR + Bidirectional Promoter
Terminator tpr + MerR+ bidirectional Promoter + RBS (Mer operon)
This part is a segment of BBa_K1355001. This biobrick has a bidirectional promoter, having dual functions: A) In reverse: transcription of the MerR regulator protein; and B) In forward: opened for insertion.
LINEAR MAP
GRAPHS
Below we can see some results for biofilm formation, it's possible to see in detail on the RESULTS page.
SECRETION MACHINERY
HlyA (BBa_K554002)
HlyA it’s a signal peptide found at α-hemolysin sequence’s C-terminal, this peptide signals for type I secretion of gram-negative bacteria. The attachment of signal peptide HlyA to the target protein, mediated by HlyB-D complex, must result in the protein transportation to the extracellular medium in a single step process. When the ligation process ends, the HlyD will induce the interaction with secretion machinery protein TolC. For the secretion process to happen, we only need the last 50-60 aa of c-terminal region of HlyA.
HlyB (BBa_K554007)
Responsible for secretion process specificity due to substrate recognition.
HlyD (BBa_K554008)
Adaptation protein, has a cytoplasmic domain followed by a membrane anchor and a large periplasmic domain.
TolC (BBa_K554009)
Channel protein located between the periplasmic region and the extracellular medium.