Coding

Part:BBa_K863022

Designed by: Isabel Huber   Group: iGEM12_Bielefeld-Germany   (2012-09-20)

bhal laccase from Bacillus halodurans with constitutive promoter J23100, RBS and HIS tag

bhal laccase with constitutive promoter J23100, RBS and HIS tag

<**Allergen characterization of BBa_K863022: Not a potential allergen

The Baltimore Biocrew 2017 team discovered that proteins generated through biobrick parts can be evaluated for allergenicity. This information is important to the people using these parts in the lab, as well as when considering using the protein for mass production, or using in the environment. The allergenicity test permits a comparison between the sequences of the biobrick parts and the identified allergen proteins enlisted in a data base.The higher the similarity between the biobricks and the proteins, the more likely the biobrick is allergenic cross-reactive. In the full-length alignments by FASTA, 30% or more amount of similarity signifies that the biobrick has a Precaution Status meaning there is a potential risk with using the part. A 50% or more amount of identity signifies that the biobrick has a Possible Allergen Status. In the sliding window of 80 amino acid segments, greater than 35% signifies similarity to allergens. The percentage of similarity implies the potential of harm biobricks’ potential negative impact to exposed populations. For more information on how to assess your own biobrick part please see the “Allergenicity Testing Protocol” in the following page http://2017.igem.org/Team:Baltimore_Bio-Crew/Experiments

For the biobrick Part:BBa_K863022, there was a 24.9 % of identity match and 50.3% similarity match to the top allergen in the allergen database. This means that the biobrick part is not of potential allergen status. In 80 amino acid alignments by FASTA window, no matches found that are greater than 35% for this biobrick. This also means that there is not of potential allergen status.


Usage and Biology

Sequence and Features


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal XbaI site found at 38
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal NheI site found at 8
    Illegal NheI site found at 31
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal XhoI site found at 219
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal XbaI site found at 38
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal XbaI site found at 38
  • 1000
    COMPATIBLE WITH RFC[1000]



First some trials of shaking flask cultivations were made with various parameters to identify the best conditions for production of the His tagged laccase Lbh1 from [http://www.dsmz.de/catalogues/details/culture/DSM-18197.html?tx_dsmzresources_pi5 Bacillus halodurans C-125 ] named BHAL. Due to inactivity of the enzyme in the cell lysate a purification method was established (using Ni-NTA-Histag resin). BHAL could not be detected by SDS-PAGE (theoretical molecular weight of 56 kDa) or activity test by using the BioBrick BBa_K863020 and E. coli KRX as expression system. Due to this results the new BioBrick BBa_K863022 was constructed and expressed E. coli Rossetta-Gami 2. With this expression system the laccase could be produced and analysed via SDS-PAGE. A small scale Ni-NTA-column was used to purify the laccase. The fractionated samples were tested regarding their activity with ABTS and showed ability in oxidizing ABTS. A scale up was not yet performed.


Cultivation, Purification and SDS-PAGE

Cultivation

The first trials to produce the Lbh1 - laccase from Bacillus halodurans (named BHAL) were performed in shaking flasks with various flask designs (from 100 mL-1 to 1 L flasks, with and without baffles) and under several conditions. The varied parameters in our screening experiments were temperature (27 °C,30 °C and 37 °C), concentration of chloramphenicol (20-170 µg mL-1), induction strategy (autoinduction and manual induction with 0,1 % rhamnose) and cultivation time (6 to 24 h). Furthermore we cultivated with and without 0.25 mM CuCl2 to provide a sufficient amount of copper, which is needed for the active center of the laccase. E.coli KRX was not able to produce active BHAL under the tested conditions, therefore another chassis was chosen. For further cultivations E. coli Rosetta-Gami 2 was transformed with BBa_K863012, because of its ability to translate rare codons. BHAL was produced under the following conditions:

  • flask design: shaking flask without baffles
  • medium: [http://2012.igem.org/Team:Bielefeld-Germany/Protocols/Materials#LB_medium LB]-Medium
  • antibiotics: 60 µg mL-1 chloramphenicol and 300 µg mL-1 ampicillin
  • temperature: 37 °C
  • cultivation time: 24 h


Purification

The cells were harvested and resuspended in Ni-NTA-equilibration buffer, mechanically lysed by sonification and centrifuged. After preparing the cell paste the BHALlaccase could not be purified with the 15 mL column, because of the column was not available. For this reason a small scale purification (6 mL) of the supernatant of the lysate was performed with a [http://2012.igem.org/Team:Bielefeld-Germany/Protocols/Production#Syringe_method 1 mL Ni-NTA-column]. The elution was collected in 1 mL fractions.

SDS-PAGE

Figure 1:SDS-PAGE of purified lysate derived from a flask cultivation of E. coli Rosetta-Gami 2 carrying BBa_K863022. Lanes 2 to 7 show the flow-through, the wash and the elution fractions 1 to 4. BHAL has a molecular weight of 56 kDa and is marked with an arrow.

In Figure 1 the different fractions of the purified cell lysate of E. coli Rosetta-Gami 2 with BBa_K863022 are shown in a SDS-PAGE. BHAL has a molecular weight of 56 kDa. In lane 5, which corresponds to the elution fraction 2, a faint band of 56 kDa is visible. Therefore the fractions were further analysed by activity test and MALDI-TOF.


Since Regionals: 12L Fermentation of E. coli Rosetta-Gami 2 with BBa_K863022

Figure 2: Fermentation of E. coli Rosetta-Gami 2 with BBa_K863022 (BHAL) in a Bioengineering NFL22. Conditions: 12 L of [http://2012.igem.org/Team:Bielefeld-Germany/Protocols/Materials#HSG_Autoinduction_medium HSG autoinduction medium] + 60 µg mL -1 chloramphenicol at 37 °C, pH 7. Agitation increased when pO2 was below 50 % and OD600 was measured each hour. The glycerin concentration was measured on important points of the cultivation with [http://2012.igem.org/Team:Bielefeld-Germany/Protocols/Analytics#Carbon_source_measurement_with_HPLC HPLC].

After measuring the BHAL activity a scale-up was performed and E. coli Rosetta-Gami 2 with BBa_K863022 was cultivated in a Bioengineering NFL 22 fermenter with a total volume of 12 L. Agitation speed, pO2 and OD600 were determined as well as the glycerin concentration. The data are illustrated in Figure 2. This time [http://2012.igem.org/Team:Bielefeld-Germany/Protocols/Materials#HSG_Autoinduction_medium HSG autodinduction medium] was used to produce more biomass. Due to the change of media and to a low amount of cells for inoculation there was a long lag phase of nearly 10 hours. During this phase the glycerin concentration was approximately constant. The following cell growth caused a decrease of glycerin concentration and of pO2. After 11 hours the value fell below 50 %, so that the agitation speed increased automatically. After 21 hours the deceleration phase started and therefore the agitation speed decreased. The maximal OD600 of 9.9 was reached after 22 hours, when the cells entered the stationary phase. The glycerin was completely consumed. The cells were harvested at this time. It might have been better to cultivate a few hours longer.


Since Regionals: Purification of BHAL

The harvested cells were resuspended in [http://2012.igem.org/wiki/index.php?title=Team:Bielefeld-Germany/Protocols/Materials#Buffers_for_His-Tag_affinity_chromatography Ni-NTA equilibration buffer] and mechanically disrupted by [http://2012.igem.org/Team:Bielefeld-Germany/Protocols/Production#Mechanical_lysis_of_the_.28bio-reactor.29_cultivation homogenization]. The cell debris were removed by centrifugation and microfiltration via [http://www.millipore.com/catalogue/module/C7493 Millipore Pellicon XL 50]. The supernatant of the cell lysate was concentrated with [http://www.millipore.com/catalogue/module/C7493 Millipore Pellicon XL 50] with 10 kDa and loaded on the Ni-NTA column (15 mL Ni-NTA resin) with a flow rate of 1 mL min-1 cm-2. Then the column was washed with 10 column volumes (CV) [http://2012.igem.org/wiki/index.php?title=Team:Bielefeld-Germany/Protocols/Materials#Buffers_for_His-Tag_affinity_chromatography Ni-NTA equilibration buffer]. The bound proteins were eluted by an increasing [http://2012.igem.org/wiki/index.php?title=Team:Bielefeld-Germany/Protocols/Materials#Buffers_for_His-Tag_affinity_chromatography Ni-NTA elution buffer] step elution from 5 % (equates to 25 mM imidazol) with a length of 80 mL, to 50 % (equates to 250 mM imidazol) with a length of 80 mL and finally to 100 % (equates to 500 mM imidazol) with a length of 90 mL. This strategy was chosen to improve the purification caused by a step by step increasing Ni-NTA-elution buffer concentration. The elution was collected in 10 mL fractions. In Figure 3 only the UV-detection signal of the wash step and the elution are shown, this is because of the high UV-detection signal of the loaded samples and to simplify the illustration of the detected product peak. A typical chromatogram of purified laccases is illustrated here. The chromatogram of the BHAL elution is shown in Figure 3:

Figure 3: Chromatogram of wash and elution fractions from FLPC Ni-NTA His-tag Purification of BHAL produced by 12 L fermentation of E. coli Rosetta Gami 2 with BBa_K863022. BHAL was eluted by a concentration of 50 % (equates to 250 mM imidazol) with a maximal UV-detection signal of 123 mAU.

The chromatogram shows two distinguished peaks. The first peak was detected at a Ni-NTA-equilibration buffer concentration of 5 % (equates to 25 mM imidazol) and resulted from the elution of weakly bound proteins. Contrary to our expectations, the chromatogram shows the second distinguished peak. This peak was detected at a [http://2012.igem.org/wiki/index.php?title=Team:Bielefeld-Germany/Protocols/Materials#Buffers_for_His-Tag_affinity_chromatography Ni-NTA-equilibration buffer] concentration of 100 % (equates to 500 mM imidazol) and resulted from the elution of bound protein. Earlier measurements of other bacterial laccases showed that the elution of these laccases begins with a elution buffer concentration of 50 %(equates to 250 mM imidazol). One explanation of this result could be a low concentration of the produced BHAL. Consequently all elution fractions were analyzed by SDS-PAGE to detect BHAL. In the chromatogram no further peaks were detected. The following increasing UV detection signal by increasing concentration of the eltutionbuffer results from the rising imidazol concentration of the Ni-NTA elution buffer. The corresponding SDS-PAGES are shown in Figure 4.


Since Regionals: SDS-PAGE of protein purification

Figure 4: SDS-PAGE of purification from the 12 L fermentations from 10/11 (BBa_K863022). Purification of the supernatant via microfiltration, diafiltration and Ni-NTA column (step gradient with 5 %, 50 % and 100 % elution buffer).

In Figure 4 the SDS-PAGE of the Ni-NTA purification of the lysed E.coli Rosetta-Gami 2 culture containing BBa_K863022 is illustrated. It shows the permeate and retentate of microfiltration and diafiltration respectively, several fractions of flow-through, wash and the elutions with different buffer concentrations respectively. The selected samples were taken where peaks were seen in the chromatogram. The His-tagged BHAL has a molecular weight of 56 kDa. Apparently the concentration of BHAL is too low to see a band.



Initial activity tests of purified fractions

The resulting fractions of the cultivation and purification of BHAL (fraction 1 to 5) were analysed with activity tests. After rebuffering into deionized H2O and incubation with 0.4 mM CuCl2 for 2 hours, the samples were measured with 140 µL sample, 0.1 mM ABTS, 100 mM sodium acetate buffer to a final volume of 200 µL. The change in optical density was measured at 420 nm, reporting the oxidation of ABTS for 5 hours at 25°C. An increase in ABTSox can be seen (Figure 5), indicating produced BHAL laccase in each fraction. Fraction 2 shows the highest amount of ABTSox (55%) reaching saturation after 3 hours. Similar to BPUL laccase, BHAL is capable to reach saturation after 3 hours with approximately oxidizing 55% of the supplied ABTS. Therefore BHAL is going to be characterized further.

Figure 5: Activity test of BHAL fractions after purification. Reaction setup includes 140 µL fraction sample (CuCl2 incubated), 0.1 mM ABTS and 100 mM sodium actetate buffer (pH 5) to a final volume of 200 µL. Measurements were done at 25°C and over a time period of 5 hours. Each fraction shows activity, especially fraction 2, which therefore contains most BHAL laccase. (n=4)


Initial activity tests of purified fractions

Different fractions of the purification of a new cultivation since the Regional Jamborees in Amsterdam were tested regarding their activity of the produced BHAL. Before and after re-buffering the protein concentration was determined. The initial activity tests were done in Britton-Robinson buffer (pH 5) with 0.1 mM ABTS at 25 °C. The protein amount was adjusted in each sample for a comparison. One distinct fraction showed the highest activity: fraction 5% 3 (Fig. 6). The contained laccase amount was calculated by assuming that the most active fraction contains 90 % laccase. This leads to a BHAL concentration of 10,9 ng mL-1.

Figure 6: Activity assay of each purified fraction of recent produced BHAL. Samples were re-buffered into H2O and the protein amount in each fraction had been adjusted. The measurements were done using the [http://2012.igem.org/Team:Bielefeld-Germany/Protocols/Analytics#General_setup_of_enzyme_activity_measurements/ standard activity assay protocol] over night. The first number indicates the percentage of used elution buffer, whereas the second number stands for the fraction number of this elution.

BHAL activity depending on different ABTS concentrations

To be able to calculate the activity in Units mg-1, measurements had to be done under substrate saturation. This allows the comparison of Units mg-1 with other laccase activities and data found in literature. For this purpose ABTS concentrations ranging from 0.1 mM to 8 mM were applied in an experimental setup containing Britton-Robinson buffer (pH) and a temperature of 25 °C. For measurements with 0.1 mM to 5 mM ABTS 616 ng BHAL were used (Fig. 7). For measurements with 5 mM to 8 mM ABTS only 308 ng BHAL were applied (Fig. 7). Applying less than 7 mM ABTS a static increase in oxidized ABTS was given. Measurements with 8 mM ABTS showed a slower increase in oxidized ABTS as with 7 mM ABTS (Fig. 8). This may be due to a substrate toxication. The most compromising ABTS concentration was 7 mM with the highest increase in oxidized ABTS. Therefore a substrate saturation was reached with 7 mM ABTS.

Figure 7: Activity assay to determine the substrate saturation with ABTS as a substrate. Measurements were done with 616 ng BHAL laccase in Britton-Robinson buffer (pH 5) at 25 °C. ABTS concentrations ranged from 0.1 mM to 5 mM.
Figure 8: Activity assay to determine the substrate saturation with ABTS as a substrate. Measurements were done with 308 ng BHAL laccase in Britton-Robinson buffer (pH 5) at 25 °C. ABTS concentrations ranged from 5 mM to 8 mM. An ABTS concentration of 7 mM was determined as substrate saturated.


BHAL pH optimum

Figure 9: Microtiter plate of the measurements for pH optimum determination. The more intensive the blue color, the more ABTS got oxidized. At pH 4 and pH 5 the darkest colour was detected.

To determine the optimal experimental setup for BHAL activity measurements, the best pH had to be determined. Using Britton-Robinson buffer pHs between pH 4 and pH 9 had been adjusted. 308 ng BHAL per well had been tested under these pH conditions using 7 mM ABTS. The CuCl2 incubated and therefor activated BHAL showed a high activity at pH 4 and pH 5, where most of ABTS was oxidized (compared to Fig. 9 and 10). The calculated specific enzyme activity of BHAL showed high activity at both mentioned pHs (Fig. 10). While BHAL had an activity of ~8 U mg-1 at pH 4 and pH 5, the enzyme activity decreased at higher pHs. At a pH of 6 only 1/3 of enzyme activity could be detected compared to the activity at pH 4 and pH 5. While still active at pH 7, the BHAL is not as suitable as thought for an application at a waste water treatment plant because of its high activity in acidic environments.

Figure 10: Oxidized ABTS by BHAL at different pH adjustments. The experimental setup included CuCl2 incubated BHAL (308 ng), Britton Robinson buffer adjusted to the tested pHs and 5 mM ABTS. Measurements were done at 25 °C for 30 minutes. The highest amount of oxidzed ABTS could be detected at pH 4 and pH 5.
Figure 11: Calculated specific enzyme activity of BHAL at different pH conditions. The highest specific enzyme activity for ABTS was under pH 4 and pH 5 conditions. The higher the pH, the less ABTS got oxidzed. One unit is defined as the amount of laccase that oxidizes 1 μmol of ABTS substrate per minute.


BHAL activity at different temperatures

Figure 12: Standard activity test for BHAL measured at 10 °C and 25 °C resulting in a decreased activity at 10 °C. As a negative control the impact of 0.4 mM CuCl2 in oxidizing ABTS at 10 °C and 25 °C was analyzed.
Figure 13: Deriving from the obtained values of oxidized ABTS in time at 10 °C and 25 °C the specific enzyme activity was calculated. For the temperatures a difference of 3 U mg-1 could be detected. One unit is defined as the amount of laccase that oxidizes 1 μmol of ABTS substrate per minute.

To investigate the activity of BHAL at temperatures that will apply at a waste water treatment plant throughout the year, activity tests were performed at 10 °C and 25 °C as described above. The measurements were conducted for 30 minutes. The obtained results revealed a lower activity of BHAL at 10 °C in comparison to 25 °C (see Fig. 12). The obtained results were used to calculate the specific enzyme activity which was at 4.2 and 7.2 U mg-1, respectively (see Figure 13). The negative control without BHAL but 0.4 mM CuCl2 at 10 °C and 25 °C showed a negligible oxidation of ABTS. The activity of BHAL was increased to about 60 % at 10 °C but nevertheless the observed activity at both conditions was great news for the possible application in waste water treatment plants.




Substrate Analysis

The measurements were made to test if the produced laccases were able to degrade different hormones. Therefore the produced laccases were inserted in the same concentrations (3 µg mL-1) to the different measurement approaches. To work with the correct pH value (which were measured by the Team Activity Test) Britton Robinson buffer at pH 5 was used for all measurements. The initial substrate concentration was 5 µg mL-1. The results of the reactions without ABTS are shown in Figure 2. On the Y-axis the percentages of degraded estradiol (blue) and ethinyl estradiol (red) are indicated. The X-axis displays the different tested laccases. The degradation was measured at t0 and after five hours of incubation at 30 °C. The negative control was the substrate in Britton Robinson buffer and showed no degradation of the substrates. The bought laccase TVEL0 which is used as positive control is able to degrade 94.7 % estradiol and 92.7 % ethinyl estradiol. The laccase BPUL (from Bacillus pumilus) degraded 35.9 % of used estradiol after five hours. ECOL was able to degrade 16.8 % estradiol. BHAL degraded 30.2 % estradiol. The best results were determined with TTHL (laccase from Thermus thermophilus). Here the percentage of degradation amounted 55.4 %.


The results of the reactions of the laccases with addition of ABTS are shown in Figure 14. The experimental set ups were the same as the reaction approach without ABTS described above. The X-axis displays the different tested laccases. On the Y-axis the percentages of degraded estradiol (blue) and ethinyl estradiol (red) are shown. The degradation was measured at t0 and after five hours of incubation at 20 °C. The negative control showed no degradation of estradiol. 6.8 % of ethinyl estradiol was decayed. The positive control TVEL0 is able to degrade 100 % estradiol and ethinyl estradiol. The laccase BPUL (from Bacillus pumilus) degraded 46.9 % of used estradiol after ten minutes incubation. ECOL was able to degrade 6.7 % estradiol. BHAL degraded 46.9 % estradiol. With TTHL (laccase from Thermus thermophilus)a degradation 29.5 % were determined.

Figure 14: Degradation of estradiol (dark green) and ethinyl estradiol (light green) with the different laccases after 5 hours without ABTS. In the graph it is shown that the bought laccase TVEL0 which was used as positive control is able to degrade more than 90 percent of the used substrates. None of the bacterial laccases are able to degrade ethinyl estradiol without ABTS but estradiol is degraded in a range from 16 %(ECOL) to 55 % (TTHL). The original concentrations of substrates were 2 µg per approach. (n = 4)
Figure 15: Degradation of estradiol (blue) and ethinyl estradiol (red) with the different laccases after 10 minutes hours with ABTS added. The commercial laccase TVEL0 which was used as positive control is able to degrade all of the used substrates. The bacterial laccase BPUL degraded 100 % of ethinyl estradiol and estradiol. ECOL the laccase from E. coli degraded 6.7 % estradiol and none of the used ethinyl estradiol. BHAL degraded 46.9 % of estradiol but no ethinyl estradiol. The laccase TTHL from Thermus thermophilus degraded 29.5 % of estradiol and 9.8 % ethinyl estradiol. The original concentrations of substrates were 2 µg per approach. (n = 4)


Immobilization

Figure 16: The percentage of laccases immobilized to CPC-Beads. 99 % of ECOL, 97 % of BPUL and 79 % of BHAL and TTHL laccases were bound to the beads.

Figure 16 shows the percentage of laccases bound after incubation with CPC-beads, relative to the original concentration. The concentration of laccases in the supernatant after incubation was measured using Roti®-Nanoquant. The results showed that only 21% of BHAL laccases was still present in the supernatant. This illustrates that BHAL was successfully immobilized on the CPC-beads.



Figure 17: Illustration of ABTS oxidation by BHAL with time compared to the negative control. The increase in ABTS oxidized proves laccase activity.

Figure 17 shows the illustration of ABTS oxidation by BHAL with time compared to the negative control. The increase in ABTS oxidized proves laccase activity even if a direct comparison with the original and not immobilized laccase solution was not possible due to the very low concentration of purified BHAL.

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