Team:UC Davis/Parts

 

New parts:

INPNC: An exogenous gene, Ice-nucleation protein (INP) from Pseudomonas syringae was suggested to be used for display of foreign proteins on the surface of E. coli. (7). Studies have shown that an INP derivative truncated at the N-and C-terminal domains can be used to display foreign proteins on the surface of E. coli. (9). We intend to use this protein to display our proteins on the cell surface before having them cleaved into the media.
We have modified this protein to be consistent with BBF RFC-12 Standard. We have submitted this part to the part registry.
For more information go to: BBa_K265008

SS: It is a derivative of PhaZ1, a polyhydroxybutarate. It allows protein fused to outer membrane proteins to become cleaved free. Because the proteins will be displayed on the cell surface, the cleavage will allow the protein to separate from the cell and take residence in the environment. This allows for a type of secretion, where a internal protein is signaled and sent into the media. We intend to use this signal sequence with both INPNC and OmpA to secrete our target protein.
We have modified this protein to be consistent with BBF RFC-12 Standard. We have submitted this part to the part registry.
For more information go to: BBa_K265002

INPNC + SS: It has been suggested that INPNC can secrete the interest gene better if it is used with the right signal sequence. Therefore, we are using INPNC and SS toegther in one of our secretion models.
We have submitted this part to the part registry.
For more information go to: BBa_K265009

OmpA + SS: Since OmpA is believed to function similarly to INPNC and INPNC believed to function better when it is used with the right signal sequence, we have decided to test and see if OmpA's ability to secret increases when it is used by a signal sequence.
We have submitted this part to the part registry.
For more information go to: BBa_K265011

RBS:  Ribosome Binding site number 32 (BBa_J61132) from the registry is being used in our secretion system.
For more information go to: BBa_J61132

Terminator: We are using BBa_B0015, a double terminator, as our terminator in both our secretion and pH system.
For more information go to: BBa_B0015

GFP (Green Fluorescent Protein) : Mutant of GFP known to be very stable (superfolder), which will let this protein fold quickly so we can use either a fluorescent reader or UV light to detect it. Therefore it has been used as a reporter in our secretion system. It also serves as a small protein in testing our secretion system.
For more informaiton go to: BBa_K265003 

Luciferase: Luciferase is a firefly protein that also fluoresces, so it serves as a reporter as well as a testable large protein.
For more information go to: BBa_1712019

LacI: One inducible Promoter which was found in the part registry.
For more information go to: BBa_R0010

6-His Tag:The 6-Histidine Tag serves as a tag for Western Blotting if our fluorescent reporters are not expressed as highly as we would like.
Note: We are using this tag, just in case if the GFP or Luciferase does not work under a plate reader.

ChvI promoter: Gene fusion studies confirmed that ChvI gene was induced by acidic conditions (1). Also, it has been known to implicate in virulence (1). This gene is one of the candidates to be use in our biological pH sensor as a promoter.

KatA promoter :This Chromosomal gene is located on the linear chromosome (2) and it seems to be induced under an acidic environment as well as being involved in the Agrobacterium tumorigenesis (2).Research has suggested that ChvG is needed for "responsiveness of  gene expression to low pH "(2). This gene has become a candidate to complete our pH sensor device from this evidence.

AopB promoter: This Chromosomal gene located on the circular chromosome (2) encodes an outer member protein exposed on the bacterial cell surface (2). Also, ChvG was shown to be absolutely required for this gene expression (2)It seems to get induced under an acidic environment as well as being involved in the Agrobacterium tumorigenesis (2). Therefore, we have chosen this gene to be one of our candidates to complete our pH sensor device.

PhoA promoter: There has been a suggestion that ChvI can activate AP activity by activating transcription of this gene, PhoA (3). Therefore, this gene has become one of our candidates to complete our pH sensor device.

ImpA promoter:Gene fusion studies confirmed that impA genes was induced by acidic conditions (1), therefore, this is one of our candidates to complete our pH sensor device.

For more information go to: UCDAVIS_Parts