Team:TU Munich/Notebook/Protocols


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1. Molecular Biology Methods

Isolation of Plasmid DNA from E.coli (miniprep)

Plasmid DNA from E. coli was isolated from overnight cultures using the DNA extraction mini-prep kit (Qiagen).The principle of this method is the alkaline lysis of the bacterial cells followed by a selective immobilization of the plasmid DNA on a column, a couple of washing steps and the elution of the DNA.

Isolation of Genomic DNA from S.cerevisiae

Determination of DNA Concentration

DNA concentration was measured using a NanoDrop Spectrophotometer by Thermo Scientific. The concentration was calculated after determination of the specific absorbance of DNA at 260 nm. Furthermore, the ratio of sample absorbance at 260 and 280 nm and at 260 an 230 nm were measured to specify the purity of the samples. A ratio of 260/280 of ~1.8 is generally accepted as “pure” for DNA. If the ratio is appreciably lower, it may indicate contemination with protein, phenol or other substances that absorb strongly at or near 280 nm. The ratio of sample absorbance at 260 and 230 nm. This is a secondary measure of nucleic acid purityad is often higher than the respective 260/280 values. They are commonly in the range of 1.8-2.2.

Agarose Gel-Electrophoresis

To separate double-stranded DNA fragments by length, agarose gel-electrophoresis using ethidium bromide as a nucleic acid stain was applied (Sambrook et al., 1989). This method was used for the restriction analysis of plasmids (analytical gel-electrophoresis) as well as for the isolation of DNA fragments (preparative gel-electrophoresis). After preparative gel-electrophoresis, the bands were cut out and purified using a Qiagen Gel extraction kit.

Polymerase Chain Reaction (PCR)

For the selective amplification of a desired DNA fragment (for example from a plasmid), the polymerase chain reaction (PCR) was used. Specially designed primers define the desired target sequence. These primers serve as starting points for the polymerase which then extends the newly synthesized DNA strand. The PCR reaction is divided in three steps which are repeated up to 30 times. Firstly, the DNA template strand is heat-denatured at 95 °C to produce single-stranded DNA. Secondly, the temperature of the reaction batch is lowered to 55 – 60 °C to allow the primers to bind. Thirdly, the temperature is raised to 72 °C. This enables the DNA polymerase to synthesize the other DNA strand.

Special PCR methods that were used include colony and genomic PCR.

purification of PCR products

PCR products were purified using the PCR purification kit by Qiagen.

Dephosphorylation of DNA

DNA restriction enzyme digest

For the preparation of DNA fragments and the restriction analysis of plasmid DNA, the DNA was cut using restriction endonucleases. For restriction digestion, buffer and DNA concentrations were used according to the suggestions by the manufacturer.

ligation / cycled ligation

After digestion with an restriction enzyme, plasmid fragments can be inserted into a vector (which was cut with the same restriction enzymes) by ligation. Ligases, such as the enzyme T4 ligase which was used in our ligations, connect complementary overhangs of fragments by catalyzing the formation of the bond between the 5'phosphoryl group and the 3' hydroxyl group.

oligohybridization of single-stranded DNA

Site-Directed Mutagenesis

Site-Directed Mutagenesis was used to mutate a specific base inside a sequence. Therefore, specific primers, which bind at the same site and contain a mismatch at the specific base are required. The original base pair that has to be replaed is replaced by the mismatch. The method works just as PCR by amplifying the desired product that contains the mismatch.Afterwards, the product ist digested with the restriction enzyme DpnI to destroy the plasmids strands which do not contain the desired base pair exchange.For the site directed mutagenesis, the QuikChange Site-Directed Mutagenesis Kit by Agilent Technologies was used.

sequencing of plasmid DNA

DNA constructs were sequenced by Eurofins mwg operon using our own sequencing primers.

gene synthesis

2. Protein Biochemical Methods

Protein expression in S.cerevisiae

Expression of our proteins was induced by transferring a overnight culture of our INVSc1 strain in glucose medium into a medium that contained galactose.In INVSc1, transcription from the GAL1 promoter is repressed in the presence of glucose. Transcription may be induced by removing glucose and adding galactose as a carbon source. Transferring cells from glucose- to galactose-containing medium causes the GAL1 promoter to become de-repressed and allows transcription to be induced.

Crude protein extraction from S.cerevisiae

To detect the recombinant protein (for example by western blot) cell lysates from our yeast transformants were prepared. Cell lysates were created using a special breaking buffer and acid-washed glass beads to break the cell wall.

SDS-Polyacrylamid-Gelelektrophoresis (SDS-PAGE)

Western Blot

Enzyme Assay and Extraction of Limonenesynthase

To test functionality of purified Limonenesynthase we used an optimized protocol of Landmann et al, 2007 . The Enzyme Assay was carried out in a total volume of 500 µl containing buffer (25 mM Tris-Cl, pH 7.5, 5 % glycerol, 1 mM DTT) supplemented with cofactors (10 mM MgCl2, 1 mg/ml BSA) with successive addition of 50 µM substrate (geranyl pyrophosphate, dissolved in DMSO) and 10 µg purified recombinant enzyme (extracted limonene synthase, after Purification). The mixture was gently overlaid with 1 ml pentane and incubated at room temperature for 15 minutes. The reaction was stopped by vigorous mixing and centrifugation (5 min, 5000g) to separate phases. The solvent phase (upper phase) was attached to a pasteur pipette containing glass wool with Sodiumsulfate for drying the solvent phase. Afterwards the combined extracts were reduced to approximately 300 µl under a stream of nitrogen. The pentane extracts were analyzed with gas chromatography-mass spectrometry to identify the enzymatically synthesized products. An aliquot of each sample (0.5 µl) was injected into "5890 Series II GC" coupled to a "Finnigan Mat 55 S MS".

Headspace GC-MS of Limonene

Because Limonene is an secretory protein [Misawa, 2011] we expected an arbitrarily amount of Limonene outside the cells. To check this predication we detected Limonene via Headspace GC-MS in the yeast cell culture supernatant. Therefore the preparatory cell culture was induced with galactose after 24 hours (see 'Protein expression in S.cerevisiae). For further 24 hours the protein expression proceeded. Afterwards the SPME needle was injected into the headspace and incubated for 30 min at 45 °C before injection into GC.

3. Microbiological Methods

cultivation of E.coli

cultivation of S.cerevisiae

heat shock transformation of E.coli with plasmid DNA

Before transformation, CaCl2 competent cells were created after Cohen et al., 1972. For the creation of competent cells, 50 ml LB medium were inoculated with an overnight culture of the used ‘’E.coli’’ strain and incubated at 37 °C, 180 rpm. After an OD 550 of 0,5 was reached, the culture was centrifuged for 4 minutes at 5000 g for 10 minutes. The pellet was then resuspended in in 40 ml pre-chilled in 0,1 M MgCl2 solution, centrifuged again and then again resuspended in 20 ml of pre-chilled 0,05 M CaCl2 solution. After 30 minutes of incubation on ice, the cells were centrifuged again and resuspenden in 2 ml 0,05 M CaCl2 solution, 15 % v/v glycerol. The competent cells were aliquoted and stored an – 80 °C. For the transformation, 100 µl competent cells and 1 ng plamid or 5 µg of a ligation product were mixed and incubated for 30 minutes on ice. Afterwards, the cells were heat shocked at 37 °C for 5 minutes, then mixed with 2 ml LB medium and incubated at 180 rpm and 37 °C for 30-45 minutes. The transformed cells were then plated on LB medium containing an antibiotic.

transformation of S.cerevisiae

Yeast cells were transformed using the S. c. EasyComp™ Transformation Kit by Invitrogen. Firstly, cells were grown in YPD medium to mid-log phase. Then, cells were pelleted and washed with a washing solution. Afterwards, cells were pelleted again and washed with Lithium cation solution in order to make the cells competent. Finally, the cells were aliquoted and stored at - 80 °C. For yeast transformation, frozen competent cells were mixed with up to 5 mg of plasmid DNA and transformation solution. The transformation batch was mixed by vortexing and incubated at 30°C to induce uptake of DNA for one hour. then the transformed cells were plated on selective plates and grwon for 2-4 days at 30 °C.

genome integration

4. Chemical Methods

Phycocyanobilin (PCB) extraction from dried Spirulina platensis powder

5. Brewing


Bacteria and yeast strains

used Plasmids


Buffer and Solutions

Microbial Media