Team:Yale/Project MAGE

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Revision as of 19:05, 31 August 2013

	Project Overview	Validate PLA synthesis	Develop bioassay	Apply MAGE	Introduce export system	Make a bioplastic

Aims for the Project

Engineer strains of E. coli to validate PLA synthesis
Develop bioassay to screen PLA production
Apply MAGE to optimize PLA production, guided by FBA
Introduce type 1 secretion system to export and extract PLA
Make a bioplastic

MAGE Targets

The first step in applying MAGE is finding MAGE targets. This involved reading numerous scientific papers learning as much as possible about the heterologous enzymes, and the pathway that was being used to create the PLA

Enzyme Targets

Sadly there was no crystal structure of either enzyme we could use to locate the sites to introduce mutations
- However, we used the literature available to locate spots where we would want to introduce mutations

Propionate CoA-transferase

According to Selmer et al. 2002, there is a catalytic glutamate found in all CoA-transferases
Using alignment tools along with the crystal structure of YdiF CoA transferase (That shares 45% sequence identity with the Propionate CoA-transferase) we were able to locate the catalytic glutamate in our enzyme
Also, we were able to locate the oxyanion hole of the enzyme
We also targeted the regions mentioned in the Lee papers
- This gave a toal of 4 MAGE oligos (CAN BE SEEN HERE)

P. resinovorans PHA synthases

From Yang et al. 2011 we knew there were 4 targets for mutation that affected the efficiency of this enzyme (E130, S325, S477, and Q481)
After some more reading we found three amino acids that were putative catalytic residues (C296, D451, and H479)
This gave the impression of one hotspot area (amino acids 477-481) so an oligo was designed to target the enzymes in between (AA478 and AA480)
- This gave a total of 10 MAGE oligos (CAN BE SEEN HERE)

Pathway Engineering

Figure 6: This figure shows how to design a oligo depending on which strand and which replichore the gene is located.

List of Papers:
Jacob et al. 1997
Matsuzaki et al. 1998
Sawers et al. 1998
Park et al. 2002
Selmer et al. 2002
Takase et al. 2002
Fong et al. 2005
Matsumoto et al. 2005
Rangarajan ES et al. 2005
Matsumoto et al. 2006
Jung et al. 2009
Matsumoto et al. 2009
Juang et al. 2010
Orth et al. 2010
Yang et al. 2011
Kandasamy et al. 2012
Yang et al. 2013

@@ Line 34: / Line 34: @@
 ==== Propionate CoA-transferase ====
 *According to Selmer et al. 2002, there is a catalytic glutamate found in all CoA-transferases
-**Using alignment tools along with the crystal structure of YdiF CoA transferase (That shares 45% sequence identity with the Propionate CoA-transferase) we were able to locate the catalytic glutamate in our enzyme
+*Using alignment tools along with the crystal structure of YdiF CoA transferase (That shares 45% sequence identity with the Propionate CoA-transferase) we were able to locate the catalytic glutamate in our enzyme
-**Also, we were able to locate the oxyanion hole of the enzyme
+*Also, we were able to locate the oxyanion hole of the enzyme
-**These two regions along with those mentioned in the Lee paper's were the targets for our MAGE oligos (4 in total)
+*We also targeted the regions mentioned in the  Lee papers
+**This gave a toal of 4 MAGE oligos (CAN BE SEEN HERE)
 |style="padding-left: 20px; padding-right: 20px;"|[[File:PCTmagetargets.jpg|400px]]
 |}
@@ Line 44: / Line 45: @@
 |-
 |
 ==== P. resinovorans PHA synthases ====
 *From Yang et al. 2011 we knew there were 4 targets for mutation that affected the efficiency of this enzyme (E130, S325, S477, and Q481)