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Team:KU Leuven/Project/Glucosemodel/MeS
From 2013.igem.org
Secret garden
Congratulations! You've found our secret garden! Follow the instructions below and win a great prize at the World jamboree!
- A video shows that two of our team members are having great fun at our favourite company. Do you know the name of the second member that appears in the video?
- For one of our models we had to do very extensive computations. To prevent our own computers from overheating and to keep the temperature in our iGEM room at a normal level, we used a supercomputer. Which centre maintains this supercomputer? (Dutch abbreviation)
- We organised a symposium with a debate, some seminars and 2 iGEM project presentations. An iGEM team came all the way from the Netherlands to present their project. What is the name of their city?
Now put all of these in this URL:https://2013.igem.org/Team:KU_Leuven/(firstname)(abbreviation)(city), (loose the brackets and put everything in lowercase) and follow the very last instruction to get your special jamboree prize!
Methyl Salicylate
Methyl salicylate is an organic ester also known as wintergreen oil. It is produced by different species of plants. It is converted from chorismate with salicylate as an intermediate. In E. coli, chorismate is used as a precursor for the amino acids phenylalanine, tryptophane and tyrosine. It is produced from erythrose-4-phosphate (Ery4P) and phosphoenolpyruvate (PEP) through the shikimate pathway (Sprenger et al., 2007). Chorismate is also the precursor of isochorismate, which is used for the biosythesis of quinones, siderophores and folic acid (Dosselaere and Vanderleyden, 2001).
Figure 1 | Methyl Salicylate
The Pathway To Methyl Salicylate
Figure 2 | The Shikimate Pathway
The conversion of Ery4P and PEP to DAHP (3-deoxy-D-arabinoheptulosonate 7-phosphate) is catalysed by DAHP synthase, an enzyme which exists in three isoforms, coded by the genes aroF, aroG and aroH. These isoforms are selectively inhibited by tyrosine, phenylalanine and tryptophan, respectively. In E. coli, about 80%, 20% and 1% of the enzyme activities are contributed by the DAHPS phenotypes of the aroG, aroF and aroH products, respectively (Ikeda et al., 2006).
This means that when there is enough phenylalanine produced by the cell, or enough present in the medium, the production of DAHP, and hence chorismate, will stop by inhibition of the aro genes. The production of phenylalanine will stop as well by inhibition of pheA, coding for chorismate mutase/prephenate dehydratase.
The conversion from chorismate to methyl salicylate starts with a conversion to isochorismate, catalysed by the enzyme isochorismate synthase, encoded by the pchA gene. This isochorismate is directly converted to salicylate by isochorismate pyruvate/lyase, encoded by the pchB gene. This conversion happens immediately, since the pchA and pchB gene form the pchBA operon which is always transcribed to one mRNA. Conversion of salicylate to methyl salicylate is catalysed by S-adenosylmethionine-dependent methyltransferase, encoded by bsmt1 (Gaille et al., 2003).
A Biobrick to start from
The iGEM team of MIT 2006 already constructed a Biobrick (BBa_J45700) encoding the pchBA and bsmt1 genes, so introducing this brick should induce the production of methyl salicylate, since chorismate is a common metabolite in E. coli. The MIT team discovered however that there was almost no methyl salicylate production observed, only when salicylic acid was added to the medium. Our experiments with this Biobrick confirmed this lack of methyl salicylate production (see the smell test in the MeS journal). There had to be something wrong with the conversion of chorismate to salicylate. One possibility is that there is something wrong with the enzymes produced by the pchBA genes. Another one is that there is a lack of chorismate present in the cell. We have attempted to increase the productivity of the MIT 2006 brick by using stronger ribosome binding sites. Also, we replaced the lac promoter by a TetR-repressible promoter, so the lacI produced in our system doesn't interfere with the transcription of pchBA. To tackle the low amount of chorismate in the cell, we have introduced an important enzyme in the chorismate pathway,a DAHP synthase encoded by aroG.
Figure 3 | The original methyl salicylate biobrick BBa_J45700
The Chorismate Problem
To overcome this problem, we looked at a study by Sun et al. (2011), in which a synthetic pathway was introduced for the production of mandelic acid from chorismate. They achieved this by deleting different genes encoding enzymes that catalyse competing pathways, as well as by introducing a feedback-insensitive DAHP synthase mutant to increase the carbon flow down the shikimate pathway. This last method gave us inspiration to overcome our own problem.
If we look at the pathway in Figure 2, we can conclude that if the amino acids are present in the medium, the conversion of chorismate to these amino acids will be inhibited allosterically, as wel as the production of DAHP. Our plan is to mutate the aroG gene in a manner that the enzymatic function still remains, but that it is insensitive to allosteric inhibition by phenylalanine. We only mutate the aroG gene since this isoform is responsible for 80% of DAHP synthase activity (Hu et al., 2003).
Figure 4 | The different pointmutations of aroG and their effect
Necessary Mutations
It is proven that a Pro150Leu point mutation is Phe-insensitive. This mutation is used as a positive control in a study by Hu et al. (2003) in which they compare the effects of different mutation in the aroG gene on the specific enzymatic activity. The results showed that a Leu175Asp mutation also lead to a Phe-insensitive enzyme. Leu175 is located at the bottom of the possible inhibitor binding pocket, and it is believed to be a critical residue.
For reasons still unknown, L175D mutation showed an increased specific enzymatic activity compared to the wild type. In more recent studies, L175D is mostly used to obtain a Phe-insensitive DAHPS (Lin et al., 2012). That is why we will try to introduce a plasmid containing a L175D mutated aroG gene.
It is also proven that transcription of the normal DAHP synthase gene will be inhibited when phenylalanine is present in the medium, so only the mutated form will be produced (Adhja & Gottesman, 1984).
Smell test
In order to test our Methyl salicylate production brick (BBa_K1060003), we we prepared 68 epps to conduct the blind smell test. This experiment consisted of 4 sets, differed in incubation time and temperature. The first set was conducted at room temperature for 24 hours, second was incubated at 37ºC for 24 hours, the third was done in 37ºC for 8 hours, the last one was carried out in room temperature for 8 hours. In each set, we inoculated our brick BBa_K1060003 with IPTG, IPTG + salicylate (concentration range from 0.01mM to 1mM), and IPTG + chorismate (concentration range from 0.01mM to 1mM), the same for MIT 2006 brick BBa_J45700. In addition, the same combinations of additives were introduced in parallel for negative control (non-MS producing E.Coli).
We had 11 people participated in the blind test, calculated the percentage of people who smelt MS. Based on the percentage, we can drive the conclusions that the smell was stronger after 24 hours incubation time compared to 8 hours. And incubating the bacteria in 37 degrees seemed to be able to enhance the production with regard to room temperature. What’s more, in the epps where 0.1mM or 1mM salicylate was added, the smell became more obvious. In addition, the effect of adding chorismate became clearer after 24 hours. The reason why chorismate requires more time to show the effect may lie in the fact that chorismate is the very first precursor of the methyl salicylate production pathway, whereas the salyciate is the precursor that one step closer to methyl salicylate. Most importantly, our brick worked in terms of producing methyl salicylate.
The results are shown below:
Figure 5 | Incubate at room temperature for 24 hours
Figure 6 | Incubate at 37 degrees for 24 hours
Figure 7 | Incubate at 37 degrees for 8 hours
