Protocols

Genetic Engineering

Whole Genome Isolation

• For the isolation following kit has been used: Fermentas GeneJET™ Plasmid Miniprep Kit
• Centrifuge 10 mL of over-night liquid culture
• Resuspend pellet in 800 µL of resuspension solution
• Ribolyse three times for 60 s with 6500 rpm (30 s break between every run, 400 mg beads)
• Centrifuge 3 min at 10,000 rpm
• Transfer 500 µL of supernatant into new 2 mL tube
• Add 500 µL of lysis buffer, invert 4 - 6 times
• Add 700 µL of neutralisation buffer, invert 4 - 6 times
• Centrifuge 10 min at 12,000 rpm
• Transfer 2 x 600 µL of supernatant into spin column (centrifuge down each time for 30 s at 12,000 rpm)
• Two wash steps with 750 µL of washing buffer
• Dry column
• Elute in 75 µL of elution buffer

Generating electrocompetent cells

• Material:
• 550 mL LB-Medium
• 1 L cooled bidest. H2O
• 150 mL cooled 10 % glycerine
• 10 pre-cooled 50 mL Falcons

• Protocol:
• Inoculate 2x3 mL LB with bacterial stock; incubate over night at 37 °C and 200 rpm
• Inoculate 2x250 mL LB with the over night cultures in 1-litre-flask at 37 °C and 140 rpm
• Incubate until OD600 0,4-0,6
• Cool the culture 15-30 minutes on ice
• Onwards all steps at 4°C
• Divide the cultures into cooled 50 mL Falcons and centrifugate at 4000 rpm, 4 °C for 15 minutes, make sure to slowly accelerate and deccelerate
• Discard supernatant
• Resuspend pellet in 5 mL cooled bidest H2O (and don't get frustrated while doing it, keep shaking gently)
• Pool two suspensions each, add bidest H2O up to 50 mL and centrifugate again (see centrifugation above)
• Discard supernatant
• Resuspend pellet in 5 mL cooled bidest H2O
• Add bidest H2O up to 50 mL and centrifugate again (see centrifugation above)
• Discard supernatant
• Resuspend pellet in 5 mL cooled 10 % glycerine
• Transfer suspensions in two 50 mL Falcons and centrifugate again (see centrifugation above)
• Discard supernatant
• Add volume of 10 % glycerine that is approximately equal to the volume of the pellet and resuspend
• Divide cells in 100 μL aliquots and freeze in liquid N2 immediately
• Store at -80 °C

Transformation via electroporation

• Thaw 50 µL competent E.coli cells on ice, dilute with icecold 50 µL glycerine (10 %) if necessary
• Add 0.5-5 µL plasmid to 50 µl electrocompetent cells
• Store cells on ice for 1 minute
• Electroporate at U = 2.5 kV, C = 25 µF, R = 400 Ώ
• Transfer transformation reaction to 450 µL SOC-Medium and shake 1 h at 37 °C
• Centrifuge 2 min at 2000 rpm and plate on selective LB-Medium
• Incubate over night at 37 °C

Analytics

SDS-PAGE

• Pouring the polyacrylamide gel
  • Make a master mix for the stacking and separating gel without adding ammonium persulfate and TEMED
  • Aliquote 6,5 mL for each separating and 2,5 mL for each stacking gel
  • Add ammonium persulfate and TEMED to each separating gel aliquote and pour the solution quickly into your gel casting form. Leave about 2 centimeters below the bottom of the comb for the stacking gel
  • Layer isopropanol on top of the gel
  • Leave the separating gel at room temperature for >60 minutes to polymerize
  • Remove isopropanol and wait until the surface is dry
  • Add ammonium persulfate and TEMED to each separating gel aliquote and pour the solution quickly into your gel casting form
  • Insert comb without getting bubbles stuck underneath
  • Leave the gel at room temperature for >60 minutes to polymerize

• For storage:
  • Remove sealing and store the gel wrapped in moistened paper towel at 4°C

• Preparing the sample
  • Mix your protein mixture 4:1 with Laemmli-buffer (30 mL protein solution + 10 mL Laemmli-buffer)
  • Heat for 5 minutes at 95 °C

• Running the gel
  • Remove sealing, put the polymerized gel into gel box and pour SDS running buffer into the negative and positive electrode chamber
  • Remove comb without destroying the gel pocket
  • Pipet the sample into the gel pockets, adjusting the volume according to the amount of protein in your sample. Make sure to include a lane with molecular weight standards (PageRuler Prestained Protein Ladder™ (Fa. Fermentas)) to determinate the molecular weight of your sample
  • Connect the power lead and run the stacking gel with 10 mA until the blue dye front enters the separating gel
  • Raise amperage up to 20 mA for running the separating gel
  • When the distance of the lowest molecular weight standard lane to the gel end is down to 0.5 cm stop the electrophoresis by turning off the power supply

NADH-Assay

• This method has been used for measurement of intracellular NADH concentration.

• Protocol:
• Inoculate an overnight culture (30 mL with 1 mL of pre-culture)
• Centrifugate (5 min at 5000 g) of 6-10 mL overnight culture (OD 4-6), adjust volume between different samples for the approximation of the number of cells
• Discard supernatant and wash pellet 3 times with 1 mL of PBS buffer
• Resuspend pellet in 1 mL PBS buffer
• Cell disruption by Ribolysation (3 x 30 sec at 6500 rpm)
• Centrifugation for 10 min at maximum speed
• Store supernatant at - 20 ° C or direct measurement with Tecan Infinite® M200 platereader

• Tecan Infinite® M200 platereader parameters:
  • Sample volume = 100 μL clear supernatant
  • Excitation = 340 nm
  • Emission = 460 nm
  • Concentration calculation by NADH calibration curve

Hexadecan Assay

• This assay has been used to measure cell membrane hydrophobicity.

• Protocol
• Inoculate an overnight culture (30 mL with 1 mL of pre-culture)
• Centrifugate (5 min at 4000 g) of 2 mL overnight culture (OD 4-6)
• Discard supernatant and wash pellet 3 times with 1 mL of PBS buffer
• Resuspend pellet in 1 mL 0,9% NaCl and measurement of OD600
• Add x μL of washed cells to 0,9% NaCl for a final volume of 3 mL . Final OD600 should be approximately 0,3 (denoted as A0, calculate exact value)
• Add 3 mL Hexadecan and vortex for 60 sec
• Incubation for 15 min
• Discard the upper organic phase and measure OD600 of the aqueous phase (denoted as A)
• Hydrophobicity can be calculated using the equation: affinity [%] = 100 x [1 – (A/A0)]

Cold osmotic shock

• Release of periplasmic protein fraction from E. coli by cold osmotic shock

• Modified protocol from Neu & Heppel (1965)
• Centrifuge E. coli cell suspension for 5 min at 14,000 g (4 °C) to collect the cells
• Discard the entire supernatant
• Resuspend the cells in ice-cold cell fractionating buffer 1. The resulting volume should be 1/4 of the former suspension volume
• Incubate for 20 min on ice. Invert the suspension at regular intervals to counteract sedimentation
• Centrifuge the cell suspension for 15 min at 14,000 g (4 °C)
• Discard the entire supernatant
• Resuspend the cells in ice-cold cell fractionating buffer 2. The resulting volume should be 1/4 of the former suspension volume
• Incubate for 10 up to 20 min on ice under regular invertion
• Centrifuge the cell suspension for 15 min at 14,000 g (4 °C)
• Save the supernatant, which contains the periplasmatic proteins and membrane proteins when using Cell fractionating buffer 2.2 and 2.3
• If the periplasmatic protein fraction is turbid, re-centrifuge and filter it through a 0.2 µm filter