The work in the Lab – catalase out of Bacillus subtilis

The goal of our lab work was the expression of catalase in the presence of the artificial amino acids ethionine and norleucine. The laboratory bacteria used (Bacillus subtilis strain from Bacillus Genetic Stock Center, http://www.bgsc.org/) should use the artificial amino acids as part of its metabolism and subsequently produce a synthetic enzyme into the nutrient solution.

The Bacilus subtilis strain used was a methionine-, tryptophan-, tyrosine- and phenylalanine-auxotroph and thusly could not survive outside of the nutrient solution.

We wanted to take advantage of the Methionauxotrophia of the selected bacterial strain. We mixed six different nutrient solutions. Three were based on the bacterium-standard solution, so-called LB, and three based on a different standard solution called M9. We included Methonine as natural amino acid in the LBM, Norleucine in the LBN, and Ethionine in the LBE. In the same fashion, M9M, M9N and M9E were produced. LBM and M9M, each with their natural Amino acid composition, were to be our reference samples; to help us know if ours could produce amylases at all: it was the so-called Control group. The mixtures are detailed in table 1.

Even though our Bacillus strain was safe, all efforts were deliberately and carefully made to avoid contamination of the outside world. All disposable items used were inactivated in Autoclaves and Certoclaves and then thrown away. Solutions with special dyes went through a special disposal process. All organisms were also put through heat sterilization for inactivation. The lab machines, work areas, lab table etc. were disinfected with a cleaning solution and the clean box was additionally treated with UV light.

Application of the pre-culture

20 micro-liters of the dry ice stored glycerin stock of Bacilus subtilis strain 1A55 are used for the application of a pre-culture. 10 ml of the LB medium (commercially available and pre-mixed) is put into a falcon tube in the clean box. Then the medium is inoculated with the glycerin stock.

Everything must remain absolutely sterile. Every tool used is either singed, treated with UV light or cleaned with 70% ethanol, even the lab gloves.

The inoculated media are left in a vibrating incubator at 37 degrees Celsius over night. The falcon tubes should be leaned on their sides to allow for a good mixture with the air. The cap is only tight enough that it stays on. This allows for air circulation.

Determining the optical concentration

To determine the optical concentration of the probe – and the resulting amount of germs it contains – 0.9 ml of germ free nutrient medium is placed in a cuvette and then 0.1 ml of the inoculated nutrient medium is added after being thoroughly mixed. With the help of a photometer, the optical concentration at 550nm of absorption is determined. 1ml of LB medium serves as a control subject. Here, everything must also be sterile to make sure hat no foreign germs make their way into the pre-culture. The cuvette no longer needs to remain sterile. It will be thrown away.

Application of the main culture

Next, the volume of the inoculum for the main culture must be calculated. The optical concentration of the main culture should be 0.1

VInokulum = (VHK*Start OD550) / OD550VK

The nutrient solution is put into the autoclaved beaker under sterile conditions. Then the calculated inoculum is moved from the pre-culture and put into the beaker. Again, cleanly work is very important and the beaker should always be covered with aluminum foil when not in the clean box. The lip and cap of every container must also be singed with flame after every time they are opened and before every time they are closed.

The beaker with the inoculated nutrient solution is put into the vibrating incubator at 37 degree Celsius. An agitator speed should be chosen that create a good amount of foam, thus aerating the culture.
1 ml of cell suspension should be moved to a cuvette under sterile conditions and the optical concentration (and with it, the cellular growth) should be determined after 1, 3, 5, 7, 20, 22 and 24 hours. Optical concentration and time are important factors for the calculation of growth curve. The samples are finally centrifuged off in the epifuge at the highest speed for 2 minutes and the cell residue transferred with a pipette to a test tube, in which they can be stored in a cool place.

Cell Harvest and the Production of Catalase

As soon as the optical concentration begins to go down, the cells have begun to die. One must act quickly, because proteinases (=enzymes that are capable of breaking apart enzymes) can get into the solution and could destroy the desired catalase. The cell suspension is then, no longer sterile, partitioned into 50ml pipettes and put into the

centrifuge at 3,500 rpm for 10 minutes. The cellular residue is, without stirring up the cell pellet, decantered off into a filter. The cellular residue extracted in this way contains all the proteins expressed by the bacteria. The filtrate is then supplemented with ammonium sulfate to turn out the catalase. This fluid is filtered two times. With the help of a dialyzation tube, the previously added ammonium sulfate is separated from the catalase. All the proteins in the substrate are separated with an SDS gel and are cooled for later analysis with the mass spectrometer at the Max-Planck-Institute.

Table 1: Mixtures

LB medium

0.5% (w/v) yeast extract

5 g/l

1% (w/v) bacto tryptone

10 g/l

1% (w/v) NaCl

10 g/l

LB+ medium

0.1% (w/v) glucose

1 g/l

L-phenylalanin

50 mg/l

L-tyrosin

50 mg/l

L-tryptophan

50 mg/l

0.5% (w/v) yeast extract

5 g/l

1% (w/v) bacto tryptone

10 g/l

1% (w/v) NaCl

10 g/l

LBM medium

LB+ Medium

100 ml

L-methionin

50 mg/l

Dissolve methionine in LB + medium and perform sterile filtration; put 2 ml in a sterile 2 ml Eppi & store it at 4 °C; use up soon; can be stored at 4 °C overnight.

LBE medium

LB+ Medium

100 ml

L-ethionin

10 g/l

Dissolve ethionine in LB + medium and perform sterile filtration; put 2 ml in a sterile 2 ml Eppi & store it at 4 °C; use up soon; can be stored at 4 °C overnight.

LBN medium

LB+ Medium

100 ml

L-norleucin

10 g/l

Dissolve norleucine in LB + medium and perform sterile filtration; put 2 ml in a sterile 2 ml Eppi & store it at 4 °C; use up soon; can be stored at 4 °C overnight.

5x M9 concentrate

Na2HPO4·2 H2O

42.5 g/l

KH2PO4

15 g/l

NH4Cl

5 g/l

NaCl

2,5 g/l

Adjust pH- value on 7.0 with NaOH; autoclave and store at room temperature.

100x micro elements solution

MnCl2·4 H2O

100 mg/l

ZnCl2

170 mg/l

CuCl2·2 H2O

43 mg/l

CoCl2·6 H2O

60 mg/l

Na2MoO4·2 H2O

60 mg/l

Perform sterile filtration; solution should be protected from UV rays and stored at room temperature.

100 mM CaCl2

CaCl2·2 H2O

1.47 g / 100 ml

Autoclave and store at room temperature.

1M MgSO4

MgSO4·7H2O

24.6 g / 100 ml

Autoclave and store at room temperature.

50 mM FeCl3

FeCl3·6H2O

1.35 g / 100 ml

Autoclave and store at room temperature.

M9 medium

5x M9 concentrate

200 ml/l

100x micro elements solution

10 ml/l

100 mM CaCl2

1 ml/l

1 M MgSO4

1 ml/l

50 mM FeCl3·6H2O

1 ml/l

L-phenylalanin

50 mg/l

L-tyrosin

50 mg/l

L-tryptophan

50 mg/l

glucose

5 g/l

Fill up to 1 l with distilled water, dissolve glucose and amino acids, perform sterile filtration and use up soon, can be stored overnight at 4 °C.

M9M medium

M9 medium

200 ml

L-methionin

50 mg/l

Dissolve methionine in M9 medium and perform sterile filtration; put 2 ml in a sterile 2 ml Eppi & store it at 4 °C; use up soon; can be stored at 4 °C overnight.

M9E medium

M9 medium

200 ml

L-ethionin

50 mg/l

Dissolve ethionine in M9 medium and perform sterile filtration; put 2 ml in a sterile 2 ml Eppi & store it at 4 °C; use up soon; can be stored at 4 °C overnight.

M9N medium

M9 medium

200 ml

L-norleucin

50 mg/l

Dissolve norleucine in M9 medium and perform sterile filtration; put 2 ml in a sterile 2 ml Eppi & store it at 4 °C; use up soon; can be stored at 4 °C overnight.