Cloning methods
The PCR Reaction System
| Components (50uL) | Volume(uL) |
|---|---|
| PrimerStar Buffer | 10 |
| dNTPs(2.5mM) | 4 |
| Primer-F(10uM) | 1 |
| Primer-R(10uM) | 1 |
| Template | 1 |
| PrimerStar | 0.5 |
| ddH2O | 32.5 |
To find the optimal temperature for our parts composite amplification, we set a gradient of annealing temperature. The result shows that 58℃ is suitable to the PCR.(Specific temperature according to different primers of components)
The double enzyme digestion system (Q.cut)
| Components (50uL) | Volume(uL) |
|---|---|
| 10 x H buffer | 5 |
| EcoRI | 1.5 |
| PstI | 1.5 |
| ddH2O | 1 |
| Conditions | 37℃ 30~40min |
The gene conjunction system
| Components (10uL) | Volume(uL) |
|---|---|
| T4 ligase | 1 |
| T4 ligase buffer | 4 |
| Linearized Vector | 0.5 |
| Insert Gene | 4.5 |
Infusion protocols
Overlap DNA segments preparation
*primer design:
Every In-Fusion primer must have two characteristics: The 5’ end of the primer must contain 15 bases that are homologous to 15 bases at one end of the DNA fragment to which it will be joined:
Fig1:Different pairing modes according to different DNA ends.
Materials：Clontech In-fusion HD Cloning Kit
| 5X In-Fusion HD Enzyme Premix | 2 μl |
| Linearized Vector * | 50~200ng |
| Purified PCR segments** | 10~200ng |
| dH2O(deionized water) | Total 10 μl |
* <10 kb: 50~100 ng,>10 kb: 50~200 ng
** <0.5Kb: 10~50ng, 0.5Kb~10Kb:50ng~100ng,>10Kb:50ng~200ng
Incubate the reaction for 15 min at 50°C, then place on ice.
Transformation into E. coli DH5a
The conjunction product was transformed into E. coli DH5a Strain. The strains were cultivated in LB plate medium containing 25ug/mL chloramphenicol at 37℃.
Reaction System of Colony PCR validation
| Components (10uL) | Volume(uL) |
|---|---|
| Es Taq Mix(2×) | 5 |
| Primer-F(10uM) | 0.3 |
| Primer-R(10uM) | 0.3 |
| ddH2O | 4.4 |
Fluorescence measurement assay
Materials: E.coli DH5α,M9 medium
Materials:
1.Inoculate 0.2% volume of bacetria containing constructed pathways into medium, meanwhile, set bacteria without the pathways as a blank control. Culture them overnight in shake incubator.
2.Inoculate 10% volume of the bacteria liquid into fresh medium and culture them to reach OD=0.6. Then dilute the liquid with corresponding medium to OD=0.1 in deep-well 96-wells plate.
3.Add inducer into the liquid under the light proof condition.The volumes are as follows:
| Bacteria | Inducer (for IAA 50μg/mL,for IPTG 1mg/mL) |
| constructed | + |
| constructed | - |
| unconstructed | + |
| unconstructed | - |
Note:Each group should set three parallels.
4. After adding the inducer,take 100μl of liquid from each well to measure fluoresence and OD.The green fluoresence should be measured at the wavelength of exciting light 485nm and emission light 518nm,while the OD should be measured at 600nm.
5. Cover the plate with tin foil and put it into the shake incubator.Take samples 30 minutes a time,then measure the fuoresence and OD following the method above.
For instrument’s setting:
| FlexStation 3 | |
|---|---|
| type | endpoint |
| Read Mode | RFUs, Top read |
| Wavelengths | |
| Emission: 518nm | |
| Excitation:485nm | |
| Cutoff: Auto | |
| Sensitivity | 6 flashes per well |
| PMT settings | Auto |
| Autocalibrate | On |
6. Deal with the data：Divide fluoresence by OD and use these results to draw curves.
Pichia expression assay
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Electroporation of Pichia
Preparation of Cells:
1. Grow 5 ml of Pichia pastoris in YPD in a 50 ml conical at 30°C overnight.
2. Inoculate 500 ml of fresh medium in a 2 liter flask with 0.1-0.5 ml of the overnight culture. Grow overnight again to an OD600 = 1.3-1.5.
3. Centrifuge the cells at 1500 x g for 5 minutes at +4°C. Resuspend the pellet with 500 ml of ice-cold, sterile water.
4. Centrifuge the cells as in Step 3, then resuspend the pellet with 250 ml of ice-cold, sterile water.
5. Centrifuge the cells as in Step 3, then resuspend the pellet in 20 ml of ice-cold 1 M sorbitol.
6. Centrifuge the cells as in Step 3, then resuspend the pellet in 1 ml of ice-cold 1 M sorbitol for a final volume of approximately 1.5 ml.
Note: You may freeze the electrocompetent cells in 80 ul aliquots; however the transformation efficiencies will decrease significantly.
Transformation:
1. Mix 80 ul of the cells from Step 6 (above) with 5-20 ug of linearized DNA (in 5-10 ul TE Buffer) and transfer them to an ice-cold 0.2 cm electroporation cuvette.
2. Incubate the cuvette with the cells on ice for 5 minutes.
3. Pulse the cells according to the parameters for yeast (Saccharomyces cerevisiae) suggested by the manufacturer of the specific electroporation device being used.
4. Immediately add 1 ml of ice-cold 1 M sorbitol to the cuvette. Transfer the cuvette contents to a sterile microcentrifuge tube.
5. Spread 200-600 ul aliquots on MD or RDB plates.
6. Incubate the plates at 28°C until colonies appear.
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Genome Isolation from Pichia
Solutions:
Minimal Medium (MD, MGY)
Sterile water
SCED (1 M sorbitol, 10 mM sodium citrate, pH 7.5, 10 mM EDTA, 10 mM DTT) Zymolyase, 3 mg/ml stock solution in water (Seikagaku America, Inc.) 1% SDS in water
5 M potassium acetate, pH 8.9
TE buffer, pH 7.4 (10 mM Tris-HCl, pH 7.4, 1 mM EDTA, pH 8.0)
7.5 M ammonium acetate, pH 7.5
Phenol:chloroform (1:1 v/v)
Preparation:
1. Grow at 30°C the recombinant strain and the parent strain to an OD600 of 5-10 in 10 ml of minimal media.
2. Collect the cells by centrifugation at 1500 x g for 5-10 minutes at room temperature.
3. Wash the cells with 10 ml sterile water by centrifugation as in Step 2.
Spheroplasting and Lysis:
1. Resuspend the cells in 2 ml of SCED buffer, pH 7.5. Make this solution fresh.
2. Add 0.1-0.3 mg of Zymolyase (mix well before adding to the cells). Incubate at 37°C for 50 minutes to achieve < 80% spheroplasting.
3.Add 2 ml of 1% SDS, mix gently and set on ice (0 to +4°C) for 5 minutes.
4. Add 1.5 ml of 5 M potassium acetate, pH 8.9, and mix gently.
5. Centrifuge at 10,000 x g for 5-10 minutes at +4°C and save the supernatant.
DNA Precipitation:
1. Transfer the supernatant from Step 5 above and add 2 volumes of ethanol. Incubate at room temperature for 15 minutes.
2. Centrifuge at 10,000 x g for 20 minutes at +4°C.
3. Resuspend the pellet gently in 0.7 ml of TE buffer, pH 7.4 and transfer to a microcentrifuge tube.
4. Gently extract with an equal volume of phenol:chloroform (1:1 v/v) followed by an equal volume of chloroform:isoamyl alcohol (24:1). Split the aqueous layer into two microcentrifuge tubes.
5. Add 1/2 volume of 7.5 M ammonium acetate, pH 7.5, and 2 volumes of ethanol to each tube. Place on dry ice for 10 minutes or at -20°C for 60 minutes.
6. Centrifuge at 10,000 x g for 20 minutes at +4°C and wash the pellets once with 1 ml of 70% ethanol. Resuspend each pellet in 50 µl of TE buffer, pH 7.5. Determine the concentration of the DNA sample. The two samples can be stored separately or combined and stored at -20°C until ready for use.
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Protein expression
After the recombinant having been confirmed by PCR.
1. Using a single colony, inoculate 25 ml of BMGY in a 250 ml baffled flask. Grow at 28-30°C in a shaking incubator (250-300 rpm) until culture reaches an OD600 = 2-6 (~16-18 hours). The cells will be in log-phase growth.
2. Harvest the cells by centrifuging at 1500-3000 x g for 5 minutes at room temperature. Decant supernatant and resuspend cell pellet to an OD600 of 1.0 in BMMY medium to induce expression (approximately 100-200 ml).
3. Place culture in a 1 liter baffled flask. Cover the flask with 2 layers of sterile gauze or cheesecloth and return to incubator to continue growth.
4. Add 100% methanol to a final concentration of 0.5% methanol every 24 hours to maintain induction.
5. At each of the times indicated below, transfer 1 ml of the expression culture to a 1.5 ml microcentrifuge tube. These samples will be used to analyze expression levels and determine the optimal time post-induction to harvest. Centrifuge at maximum speed in a microcentrifuge for 2-3 minutes at room temperature. Time points (hours): 0, 6, 12, 24, 36, 48, 60, 72, 84, and 96.
6. For secreted expression, transfer the supernatant to a separate tube. Store the supernatant and the cell pellets at -80°C until ready to assay.
7. Analyze the supernatants and cell pellets for protein expression by Coomassiestained SDS-PAGE and Western blot or functional assay .
SDS-PAGE protocol:
Stock Solutions:
1) 1.5M TrisHCl pH 8.3 + 0.4% SDS (adjust pH before you add the SDS). Keep RT.
2) 30% Acrylamide 0.8% Methylene bis Acrylamide or 40% Acrylamide / Methylene bis Acrylamide (ratio: 37.5:1). Keep 4°C
3) 0.5M TrisHCl pH 6.8+ 0.4% SDS (adjust pH before you add the SDS). Keep RT.
4) 10% Ammonium Persulfate (APS). Keep 4°C less than 1 month.
Running Buffer x5:
| Trizma | 0.125M | 15.1gr |
| Glycine | 0.96M | 72.0gr |
| SDS | 0.5% | 5.0gr |
| ddH2O up to | 1L | |
Keep at RT.
Dissolving (Sample) Buffer x5:
| Glycerol | 5mL |
| SDS | 1gr |
| ß Mercapto Ethanol (or 0.25M DTT) | 2.56mL |
| 0.5M TrisHCl pH 6.8+ 0.4% SDS | 2.13mL |
| Bromo Phenol Blue | traces |
Keep in aliquots of 1mL at -20C
Separating Gel:
| % Acrylamide | 10% | 10% | 12% | 12% | 15% |
| Number of Minigels | 5 | 8 | 5 | 8 | 5 |
| 1.5M TrisHCl pH 8.3 + 0.4% SDS | 7.0 mL | 10.5 mL | 7.0 mL | 10.5 mL | 7.0 mL |
| 30% Acrylamide 0.8% Methylene bis Acrylamide | 9.3 mL | 13.9 mL | 11.3 mL | 16.9 mL | 13.9 mL |
| H2O | 12.3 mL | 18.4 mL | 9.3 mL | 13.9 mL | 6.3 mL |
| 10% APS | 100 uL | 150 uL | 100 uL | 150 uL | 100 uL |
| TEMED | 23 uL | 35 uL | 23 uL | 35 uL | 23 uL |
| % Acrylamide | 10% | 10% | 12% | 12% | 15% |
| Number of Minigels | 5 | 8 | 5 | 8 | 5 |
| 1.5M TrisHCl pH 8.3 + 0.4% SDS | 7.0 mL | 10.5 mL | 7.0 mL | 10.5 mL | 7.0 mL |
| 40% Acrylamide / Methylene bis Acrylamide (ratio: 37.5:1) | 7.2 mL | 10.8 mL | 8.6 mL | 12.9 mL | 10.8 mL |
| H2O | 14.4 mL | 21.5 mL | 12 mL | 17.9 mL | 9.4 mL |
| 10% APS | 100 uL | 150 uL | 100 uL | 150 uL | 100 uL |
| TEMED | 23 uL | 35 uL | 23 uL | 35 uL | 23 uL |
Add TEMED and APS at the end. Gently swirl the flask to mix, being careful not to generate bubbles. Pipette the solution to a level of 4cm of the top. Add 0.3mL of n-buthanol. A very sharp liquid interface will be visible within 10-20min. Let polymerize the gel for another hour at least. Rinse the surface of the gel with watter before pouring the stacking gel.
Stacking Gel :
| Number of Minigels | 2 | 5 | 8 |
| 0.5M TrisHCl pH 6.8 + 0.4% SDS | 2.5 mL | 4.0 mL | 5.2 mL |
| 30% Acrylamide 0.8% Methylene bis Acrylamide | 1.0 mL | 1.5 mL | 2.0 mL |
| H2O | 6.4 mL | 9.6 mL | 12.8 mL |
| 10% APS | 100 uL | 150 uL | 200 uL |
| TEMED | 10 uL | 15 uL | 20 uL |
| Number of Minigels | 2 | 5 | 8 |
| 0.5M TrisHCl pH 6.8 + 0.4% SDS | 2.5 mL | 4.0 mL | 5.2 mL |
| 40% Acrylamide / Methylene bis Acrylamide (ratio: 37.5:1) | 0.75 mL | 1.1 mL | 1.4 mL |
| H2O | 6.6 mL | 10 mL | 13.4 mL |
| 10% APS | 100 uL | 150 uL | 200 uL |
| TEMED | 10 uL | 15 uL | 20 uL |
Fill each sandwich with stacking gel solution and insert a comb into each place taking care not to trap any bubbles bellow the teeth. The gel should fully polymerized after 1hour. Cover gel with a nylon wrap. Keep gels no more than 2 weeks at 4°C.
Sample Preparation:
Prior to adding the sample buffer, keep samples at 0°C. Add the SDS sample buffer (RT) to the sample (still on ice), and boil at 100°C immediately 3 to 5 min.
*Do not leave the sample in SDS sample buffer without heating; endogenous proteases are very active in SDS sample buffer and can cause severe degradation. Once heated, sample could sit at RT for a short time until loading, or at -20°C for a long time.
For a gel thickness of 0.75mm and 15 wells applied 10-25ug protein of a complex mixture, when staining with Coomasie Blue and 0.5 to 5ug for samples for one or few proteins. If silver stain is used 10 to 100-fold less protein can be used.
Samples can be concentrated or interferences (salts, etc.) eliminated with TCA, acetone, TCA-DOC, ethanol, etc. (see attached Protocol). Potassium ions in particular must be removed since they precipitate the SDS. Some proteins such as nuclear non-histone proteins and membrane proteins, require the presence of 8M urea in the SDS sample buffer to get complete solubilization.
Some membrane bound proteins undergo aggregation at temperatures above 40-50°C. In this case incubate 30min at 40°C with sample buffer. A shift in the migration distances of proteins with internal disulfide bridges could be observed by incubating samples in SDS in the presence or absence of reducing agents (mercaptoethanol, DTT, DTE, etc)
Staining Solution :
| Methanol CP | 500mL | 50% |
| Acetic Acid CP | 100mL | 10% |
| H2O | 400mL | |
| Coomasie Brilliant Blue R | 2.5gr | 0.25% |
Keep flask on dark at RT
Destaining Solution:
| Methanol CP | 150mL | 15% |
| Acetic Acid CP | 100mL | 10% |
| H2O | 750mL | |
Keep flask on dark at RT
Stain overnight at RT or put gel with staining solution 8 sec in microwave on the high position, and then shake for another 15min at RT. Wash with water 2-3 times and distain by several changes of destaining solution in the presence of a sponge.
Protein BCA quantification assay
Equipment:
Multiskan plate reader, TaKaRa BCA Protein Assay Kit (No. T9300A), transparent 96-well plate, Amicon Ultra -4mL Millipore
Sample preparation:
1. Culture yeast strain(Y.Lipolytica) in 5ml YPD medium,30℃,200r/min,overnight.
2. Transfer 1% culture to 50ml YPD for amplification,30℃,200r/min,cultivate for 60~70h.
3. Centrifuge the sample at 3000rpm to collect supernatant.
4. Get 8 times concentrated sample by ultrafiltration (MWCO 19kDa,3000rpm,4℃).
Measuring:
1. Make working reagent, BCA kit,A reagent and B reagent mix with ratio 100:1.
2. Dilute protein standard reagent in 96-well plate to make standard curve.
3. Add 50ul concentrated samples in 96-well plate for each 3 parallels.
4. Add 200ul working reagent, vibrate to mix up,incubate in 37℃ for 30min.
5. Take YPD medium as blank to measure 562nm absorption under Multiskan plate reader.
Sand cementation test assay
Experiments were conducted at 28°C on a set of experimental devices made up with a peristaltic pump, a holder support and a 20 mL glass syringe with gauze pad at the bottom and quartz sand filled in the syringe (4 g 100 mesh particles and 36 g 60 mesh particles). The sand was rinsed with distilled water and bubbles were exhausted. Then, another gauze pad was used to cover the sand. Fifteen mL of test or control cell culture was added to the syringes by peristaltic pump at maximum speed and incubated for 2 hrs. Then, 20 mL of 1:1 mixture of 25 mM Tris-HCl pH 7.5 and 200 mM CaCl2 were added to the syringe and incubated for 2 hrs. This mixture was changed 20 times and then rinsed once with distilled water. The top gauze was removed, and the glass syringe with sand was dehydrated for 1 day in a drying oven at 120°C. Then, the sand could be removed from the syringe. The relative intensity of each cylinder was quantified using the critical pressure value at cylinder destruction and then normalized to the value of the Si-tag1+2+3 group. The sand cementation test under high water-to-sand ratio with turbulence was conducted in flasks on a shaker set at 50 rpm. Sand samples treated with different cell suspensions were checked under a normal microscope.
