Team:St Andrews/Omega-3-synthesis

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Omega-3 fatty acid synthesis

ω-3 fatty acids are a key component of the human diet. Our team is recreating this synthetic pathway in E. coli, using genes from the cyanobacteria Synechocystis and the trypanosomatid Leishmania major. Combining the DNA code for elongase and desaturase enzymes, we can convert the plain fatty acid of E. coli into highly valuable ω-3 fatty acids.

  • Figure 1: "Synechocystis sp."

  • Figure 2: "Trypanosome cruzi"

  • Figure 3: "Leishmania major"

Omega-3 fatty acids are an essential part of the human diet (Bender, Bender, 1999). Human beings, like all larger organisms, cannot synthesize ω-3 fatty acids, This is due to a lack of the enzyme Δ15 desaturase, which creates a double bond at the 15th carbon of a long-chain fatty acid. Certain micro-organisms, such as microalgae and cyanobacteria, do contain this desaturase and can thus directly synthesize ω-3 fatty acids (Arts et al., 2009). ω-3 fatty acids then enter the food chain – algae are eaten by fish, and seafood is subsequently the main source of ω-3 for humans (Tonon et al., 2002).

However, the current economic policies of overfishing are a serious contributor to marine biodestruction. As the human population is estimated to rise to 9.1 billion by 2050 (Cohen, 2003), pressure on fish stock will increase. Additionally, global warming will reduce the availability of ω-3 (Arts et al., 2009): at higher temperatures, microalgae produce less ω-3 desaturated fatty acids. Desaturated carbon chains cause a lower melting temperature in the membrane, which the microorganism wants to avoid by synthesizing more saturated fatty acids in their membranes (Garwin, Cronan, 1980). Thus, the combination of declining fish stock and a decrease in overall ω-3 fatty acids is making the supply for human nutrition a relevant issue.

Harvesting algae directly is costly and ineffective (Borowitzka, 1997). There is much potential in expressing a metabolic pathway for ω-3 fatty acid synthesis in E. coli, which is cheaper and more accessible.

Figure 4: "The metabolic pathway to ω-3 fatty acids"

Figure 4 shows the elongation and desaturation enzymes necessary to convert an 18:1 fatty acid, which E. coli synthesizes, into an poly-unsaturated fatty acid.

modified from Livore et al., 2006

E. coli naturally synthesize poly-unsaturated fatty acids up to a carbon chain length of 18, with a single desaturation (18:1) (Marr, Ingraham, 1969). Valuable ω-3 fatty acids require a double bonds at the third carbon from the end of its carbon chain and can have >20 carbons.

In order to have E. coli synthesize ω-3 fatty acids, we needed to introduce enzymes that could elongate and desaturate fatty acid substrates (cf. Fig. 4).

The genes for Δ12, Δ15 (ω6) and Δ6 were obtained from Synechocystis sp., a cyanobacterium. The trypanosomatid Leishmania major provided the DNA for the ELO 6 gene. Additionally, we used Trypanosome cruzi as a secondary source of Δ12.

However, our first successful ligations of Δ12 did not yield us with the expected 18:2 fatty acid. We hypothesized that E. coli’s inherent 18-carbon chain fatty acid might not be suited as a substrate for Δ12 – the double bond is in a different position, the 11th. Therefore, we "fed" our cells with suitable 18:1, to then observe 18:2 fatty acid, and ultimately ω-3 desaturation, in the mass spec results!

The following genes were employed (please click for sequences and KEGG numbers):

Δ6 Synechocystis Δ12 Synechocystis Δ15 Synechocystis ELO 6 L. major Δ12 T. Cruzi

These genes were amplified through PCR (Promega, GoTaq HotStart) at temperatures 48°C and 56°C.

We were able to ligate these genes into pET-15b vector first. After a number of expression attempts, some initial conclusions were reached. All experiments done on ELO6 failed. Also, Δ12 from T. cruzi gave overall weaker results than the same gene from Synechocystis. As such, latter work was only carried out on genes from Synechocystis.

Δ6, Δ12, and Δ15 desaturases were successfully ligated into two distinct pET-Duet vectors (vectors with two multicloning sites), one of them containing Δ12 and Δ15 desaturases, and the other Duet vector ligated only to Δ6 desaturase.

After transformation into cell strain BL21(DE3), even though protein expression was clear, functionality could not be established. It was hypothesized that the naturally-occuring 18:1 fatty acid in E. coli is the wrong substrate for the desaturases. This fatty acid has its desaturation at the 11th carbon. Thus, the E. coli were fed 18:1 (Δ9).

Characterisation followed by analysing lipid composition of transformed E. coli. Lipid profiles of membrane assays and lipid extracts from cells were obtained using Fatty Acid Methyl Ester (FAME) Analysis by GC-MS.

After characterization, we finally ligated separately each of our desaturases into the submission vector pSB1C3.

    Fig. 5: "UV photograph of PCR results"

    The figure shows the results of a PCR extraction of our genes of choice, done with GoTaq HotStart PCR kit at 2 different annealing temperatures: Δ12 (48°C) - Δ12 (56°C) - Δ15 (48°C) - Δ15 (56°C) - Δ6 (48°C) - Δ6 (56°C).

Primers

All primers are notated 5' to 3'. Initially, we worked with NdeI and XhoI as the restriction sites.

Δ12 T. Cruzi forward
Δ12 T. Cruzi reverse
Δ12 Synechocystis forward
Δ12 Synechocystis reverse
Δ15 Synechocystis forward
Δ15 Synechocystis reverse
Δ6 Synechocystis forward
Δ6 Synechocystis reverse
ELO6 L. major forward
ELO6 L. major reverse

When using the pET-duet vector, we needed additionally primers for the alternative restriction sites and His-tags. For Δ6 and Δ12, we cut with HindIII and EcoRI; NdeI and XhoI were used for Δ15 and ELO6.

ELO6 L. major forward
Δ15 Synechocystis sp. forward
Δ6 Synechocystis sp. forward
Δ6 Synechocystis sp. reverse
Δ12 Synechocystis sp. forward
Δ12 Synechocystis sp. reverse

For the submission vector, we once again required new primers, using restriction sites EcoRI and PstI. For Δ6 and Δ12 forward, we used the primers from the duet vector (see above).

Δ6 Synechocystis reverse
Δ15 Synechocystis forward
Δ15 and Δ12 Synechocystis reverse

Analysis

Lipid Analysis

Lipids were extracted from transformed E. coli using the Blight/Dyer method. (Please refer to the Lipid extraction lab book entry for further detail.)

Mass Spectrometry

Lipids were extracted from transformed E. coli using the Blight/Dyer method. (Please refer to the Lipid extraction lab book entry for further detail.)

We then analyzed the the fatty acid content of the transformed cells to determine whether it differed from the previously analyzed background lipid composition. This was done using mass spectrometry.

Bradford protein assay

A Bradford protein assay was carried out to asses protein concentration (Bradford, 1976).

Sequencing

We sent off samples to GATC for sequencing.

By combining a number of genes, we were able to partially recreate the pathway described above (Fig. 4).

Due to time constraints, we were unable to submit a BioBrick containing all of the genes we expected to in order to have a single BioBrick that could encode all of the desaturases needed to obtain an ω-3 biosynthetic pathway.However, we were able to express and characterise Δ12, Δ15 and Δ6 desaturases, the first three enzymes involved in ω-3 biosynthesis. As shown in charts 2, 3 and 4 the presence of alpha-linoleic acid (18:3Δ9,12,15), an omega-3 fatty acid, can be observed in in E. coli, which does not occur naturally in their bacterial membrane.

Mass Spectrometry

Bradford protein assay

    Chart 1: "Bradford protein assay"

    This chart shows the results of a Bradford protein assay. It was carried out on the following ligated plasmids transformed into BL21: Δ12 in pET-15b (in 2 colonies), Δ12 in pLYS, Δ12 in pET-duet (in 2 colonies), Δ6 in pET-duet, Δ12/Δ15 in pET-duet (in 2 colonies).

The Bradford protein assay discuss results

We have submitted 3 BioBricks involved in the ω-3 biosynthetic pathway to the Registry of Standard Parts:

Biobrick Short name Description Length
BBa_K925000 Delta-12 desaturase Desaturase introducing a double bond at the Δ-12 site in the hydrocarbon chain of oleic acid (18:1, Δ9) to give linoleic acid (18:2 Δ9,12) 1056
BBa_K925001 Delta-15 desaturase Desaturase introducing a double bond at the Δ-15 site in the hydrocarbon chain of linoleic acid (18:2 ; Δ9,12) for its convertion into alpha-linoleic acid (18:3 ; Δ9,12,15), an ω -3 PUFA 1080
BBa_K925003 Delta-6 desaturase Desaturas introducing a double bond at the Δ-12 site in the hydrocarbon chain of oleic acid (18:1, Δ9) to give linoleic acid (18:2 Δ9,12) 1080

Arts, et al., 2009. Lipids in Aquatic Ecosystems. New York. Springer.

Bender D. A. and Bender, A. E, 1999. Benders' dictionary of nutrition and food technology. Cambridge: CRC Press.

Bradford, M., 1976. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem, 7;72:248-54.

Cohen, J., 2003. Human Population: The Next Half Century. Science, New Series, Vol. 302, No. 5648. Pp. 1172-1175.

Garwin J. L. and Cronan J. E. Jr, 1980. Thermal modulation of fatty acid synthesis in Escherichia coli does not involve de novo enzyme synthesis. J Bacteriol, 141(3): 1457–1459.

Livore V., Tripodi K., Utarro A., 2007. Elongation of polyunsaturated fatty acids in trypanosomatids. FEBS Journal, 274: 264–274.

Marr A., Ingraham J., 1969. Effect of temperature on the composition of fatty acids in Escherichia coli. J. Bactiol. 84(6). Pp. 1260–1267.

Tonon T., et al., 2002. Long chain polyunsaturated fatty acid production and partitioning to triacylglycerols in four microalgae. Phytochemistry, Vol 61 Iss 1. Pgs 15-24.

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University of St Andrews, 2012.

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This iGEM team has been funded by the MSD Scottish Life Sciences Fund. The opinions expressed by this iGEM team are those of the team members and do not necessarily represent those of Merck Sharp & Dohme Limited, nor its Affiliates.