Team:Bielefeld-Germany/Results/pumi
From 2012.igem.org
Summary
First some trials of shaking flask cultivations were made with different parameters to define the best conditions for production of the His tagged CotA from [http://www.dsmz.de/catalogues/details/culture/DSM-27.html Bacillus pumilus DSM 27 ( ATCC7061)] named BPUL. Due to inactivity of the enzyme in the cell lysate a purification method was established (using Ni-NTA-Histag resin and Syringe or ÄKTA method). The purified BPUL could be detected by SDS-PAGE (molecular weight of 58.6 kDa) as well as by MALDI-TOF. To improve the purification strategies the length of the linear elution gradient was increased up to 200 mL . The fractionated samples were also tested concerning their activity and revealed high activity. Optimal conditions for activity were identified. After measuring activity of BPUL a successful scale up was made up to 3 L and also up to 6 L that enables an intense screening afterwards. The scale up will be important for a further application.
Cultivation, Purification and SDS-PAGE
Shaking Flask Cultivation
The first trials to produce the CotA-laccase from [http://www.dsmz.de/catalogues/details/culture/DSM-27.html Bacillus pumilus DSM 27] (ATCC7061, named BPUL) were performed in shaking flasks with various designs (from 100 mL-1 to 1 L flasks, with and without baffles) and under different conditions. The parameters tested during the screening experiments were temperature (27 °C,30 °C and 37 °C), the concentration of chloramphenicol (20 to 170 µg mL-1), induction strategy (autoinduction and manual induction with 0,1 % rhamnose) and cultivation time (6 to 24 h). Furthermore it was 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. Based on the screening experiments the best conditions for expression of BPUL were identified(see below). The addition of CuCl2 did not increase activity, so it was omitted.
- flask design: shaking flask without baffles
- medium: autoinduction medium
- antibiotics: 60 µg mL-1 chloramphenicol
- temperature: 37 °C
- cultivation time: 12 h
The reproducibility of the measured data and results were investigated for the shaking flask and bioreactor cultivation.
3 L Fermentation E. coli KRX with <partinfo>BBa_K863000</partinfo>
After the measurement of BPUL activity we made a scale-up and fermented E. coli KRX with <partinfo>BBa_K863000</partinfo> in aBraun Biostat B fermenter with a total volume of 3 L. Agitation speed, pO2 and OD600 were determined and illustrated in Figure 1. We got a long lag phase of 2 hours due to a relatively old preculture. The cell growth caused a decrease in pO2 and after 3 hours the value fell below 50 %, so that the agitation speed increased automatically. After 8.5 hours the deceleration phase started and therefore the agitation speed was decreased. The maximal OD600 of 3.53 was reached after 10 hours, which means a decrease in comparison to the fermentation of E. coli KRX under the same conditions (OD600,max =4.86 after 8.5 hours, time shift due to long lag phase). The cells were harvested after 11 hours.
Purification of BPUL
The harvested cells were resuspended in Ni-NTA-equilibrationbuffer, mechanically lysed by homogenization and cell debris were removed by centrifugation. The supernatant of the lysed cell paste was loaded on the Ni-NTA-column (15 mL Ni-NTA resin) with a flowrate of 1 mL min-1 cm-2. The column was washed with 10 column volumes (CV) Ni-NTA-equilibrationbuffer. The bound proteins were eluted by an increasing Ni-NTA-elutionbuffer gradient from 0 % to 100 % with a total volume of 100 mL and the elution was collected in 10 mL fractions. Due to the high UV-detection signal of the loaded samples and to simplify the illustration of the detected product peak only the UV-detection signal of the wash step and the elution are shown. A typical chromatogram of purified laccases is illustrated here. The chromatogram of the BPUL-elution is shown in Figure 2:
The chromatogram shows a remarkable widespread peak between the process volume of 460 mL to 480 mL with the highest UV-detection signal of 69 mAU, which can be explained by the elution of bound proteins. The corresponding fractions were analyzed by SDS-PAGE analysis. During the elution, a steady increase of the UV-signal caused by the increasing imidazol concentration during the elution gradient. Between the process volume of 550 and 580 mL there are several peaks (up to a UV-detection-signal of 980 mAU) detectable. These results are caused by an accidental detachment in front of the UV-detector. Just to be on the safe side, the corresponding fractions were analyzed by SDS-PAGE analysis. The corresponding SDS-PAGE is shown in Figure 3.
SDS-PAGE of purified BPUL
Figure 3 shows the purified ECOL including flow-through, wash and the elution fractions 7 and 8. These two fractions were chosen due to a high peak in the chromatogram. BPUL has a molecular weight of 58.6 kDA and was marked with a red arrow. The band appears in both fractions. There are also some other non-specific bands, which could not be identified. To improve the purification the elution gradient length should be longer and slower the next time.
The appearing bands were analyzed by MALDI-TOF and could be identified as CotA (BPUL).
6 L Fermentation of E. coli KRX with <partinfo>BBa_K863000</partinfo>
Another scale-up for E. coli KRX with <partinfo>BBa_K863000</partinfo> was made up to a final working volume of 6 L in a Bioengineering NFL22. Agitation speed, pO2 and OD600 were determined and illustrated in Figure 4. There was no noticeable lag phase. Agitation speed was increased up to 425 rpm after one hour due to problems caused by the control panel. The pO2 decreased until a cultivation time of 4.75 hours. The increasing pO2 level indicates the beginning of the deceleration phase. There is no visible break in cell growth caused by an induction of protein expression. A maximal OD600 of 3.68 was reached after 8 hours of cultivation, which is similar to the 3 L fermentation (OD600 = 3.58 after 10 hours, time shift due to long lag phase). The cells were harvested after 12 hours.
Purification of BPUL
The harvested cells were prepared in Ni-NTA-equilibrationbuffer, mechanically lysed by homogenization and cell debris were removed by centrifugation. The supernatant of the lysed cell paste was loaded on the Ni-NTA-column (15 mL Ni-NTA resin) with a flow rate of 1 mL min-1 cm-2. The column was washed with 5 column volumes (CV) Ni-NTA-equilibrationbuffer. The bound proteins were eluted by an increasing elutionbuffer gradient from 0 % (equates to 20 mM imidazol) to 100 % (equates to 500 mM imidazol) with a length of 200 mL. This strategy was chosen to improve the purification by a slower increase of Ni-NTA-elutionbuffer concentration. The elution was collected in 10 mL fractions. Due to the high UV-detection signal of the loaded samples and to simplify the illustration of the detected product peak only the UV-detection signal of the wash step and the elution are shown. A typical chromatogram of purified laccases is illustrated here. The chromatogram of the BPUL elution is shown in Figure 5.
The chromatogram shows a peak at the beginning of the elution. This can be explained by pressure fluctuations upon starting the elution procedure. In between the processing volumes of 832 mL and 900 mL there is remarkable widespread peak with a UV-detection signal of 115 mAU. This peak corresponds to an elution of bound proteins at a Ni-NTA elution buffer concentration between 10 % and 20 % (equates to 50-100 mM imidazol). The corresponding fractions were analyzed by SDS-PAGE. The ensuing upwards trend of the UV-signal is caused by the increasing imidazol concentration during the elution gradient. Towards the end of the elution procedure there is a constant UV-detection signal, which shows, that most of the bound proteins was already eluted. Just to be on the safe side, all fractions were analyzed by SDS-PAGE to detect BPUL. The SDS-PAGE is shown in Figure 6.
SDS-PAGE of purified BPUL
In Figure 6 the SDS-PAGE of the Ni-NTA purification of the lysed E. coli KRX culture containing <partinfo>BBa_K863000</partinfo> is illustrated. It shows the flow-through, wash and elution fractions 1 to 9. The His-tagged BPUL has a molecular weight of 58.6 kDA and was marked with a red arrow. The band appears in all fractions from 2 to 9 with varying strength, the strongest ones in fractions 7 to 9. There are also some other non-specific bands, which could not be identified. Therefore the purification method could moreover be improved. In summary, the scale up was successful, improving protein production and purification method once again.
Furthermore the bands were analyzed by MALDI-TOF and identified as CotA (BPUL).
Since Regionals: 12 L Fermentation E. coli KRX with <partinfo>BBa_K863000</partinfo>
After the positive measurement of activity of ECOL we made a scale-up and fermented E. coli KRX with <partinfo>BBa_K863000</partinfo> in an Infors Labfors fermenter with a total volume of 3 L. Agitation speed, pO2 and OD600 were determined and illustrated in Figure 1. The exponential phase started after 1.5 hours of cultivation. The cell growth caused a decrease in pO2. After 2 hours of cultivation the agitation speed increased up to 629 rmp (5.9 hours) to hold the minimal pO2 level of 50 %. Then, after 4 hours there was a break in cell growth due to induction of protein expression. The maximal OD600 of 2.78 was reached after 5 hours. In comparison to E. coli KRX (OD600,max =4.86 after 8.5 hours) and to E. coli KRX with <partinfo>BBa_K863000</partinfo> (OD600,max =3.53 after 10 hours, time shift due to long lag phase) the OD600 max is lower. In the following hours, the OD600 and the agitation speed decreased and the pO2 increased, which indicates the death phase of the cells. This is caused by the cell toxicity of ECOL (reference: [http://www.dbu.de/OPAC/ab/DBU-Abschlussbericht-AZ-13191.pdf DBU final report]). Hence, cells were harvested after 12 hours.
Since Regionals: Purification of BPUL
MALDI-TOF Analysis of BPUL
The E. coli laccase was identified using the following software
- FlexControl
- Flexanalysis and
- Biotools
from Brunker Daltronics.
The in silico- tryspinated created peptide mass fingerprints were compared with the measured masses gotten from the MALDI. With a sequence coverage of 21,9% BPUL was identified.
In Figure 7 and 8 the chromatogram of the peptide mass fingerprint and the single masses are shown.
Activity analysis of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K863000 BPUL]
Initial activity tests of purified fractions
Initial tests were done with elution fractions 1 to 4 to determine the activity of the purified [http://partsregistry.org/wiki/index.php?title=Part:BBa_K863000 BPUL] laccase. The fractions were rebuffered into deionized H2O using [http://www.sigmaaldrich.com/content/dam/sigma-aldrich/docs/Supelco/Product_Information_Sheet/4774.pdf HiTrap Desalting Columns] and incubated with 0.4 mM CuCl2. The reaction setup included 140 µL of a elution fraction, 0.1 mM ABTS and 100 mM sodium acetate buffer (pH 5) to a final volume of 200 µL and the absorption was measured at 420 nm to detect oxidization over a time period of 5 hours at 25°C. Each fraction did show contained active laccase able to oxidize ABTS (see Figure 9). After 15 minutes, saturation was observed with ~60 µM oxidized ABTS. After 5 hours ~5 µM ABTS got reduced again. This behavior has been observed in the activity plot of the positive control TVEL0 before, indicating, that the oxidation catalyzed by this laccase seems is reversible. Additionally, protein concentrations of each fraction were identified using the Bradford protocol. The four tested fractions showed approximately the same amount of protein after rebuffering, namely 0.5 mg mL-1. Fraction 4, containing the most protein and also most of active laccase was chosen for subsequent activity tests of BPUL. The protein concentration was reduced to 0.03 mg mL-1 for each measured sample to allow a comparison between TVEL0 measurements and [http://partsregistry.org/wiki/index.php?title=Part:BBa_K863000 BPUL] measurements.
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K863000 BPUL] pH optimum
To determine at which pH the [http://partsregistry.org/wiki/index.php?title=Part:BBa_K863000 BPUL] laccase has its optimum in activity, a gradient of sodium acetate buffer pHs was prepared. Starting with pH 1 to pH 9 [http://partsregistry.org/wiki/index.php?title=Part:BBa_K863000 BPUL] activity was tested using the described conditions above and 0.03 mg mL-1 protein. The results are shown in Figure 11. A distinct pH optimum can be seen at pH 5. The saturation is reached after 3 hours with 50% oxidization of ABTS through the [http://partsregistry.org/wiki/index.php?title=Part:BBa_K863000 BPUL] laccase at pH 5 (55 µM oxidized ABTS). The other tested pHs only led to a oxidation of 18% of added ABTS. Figure 12 represents the negative control showing the oxidation of ABTS through 0.4 mM CuCl2 at the chosen pHs. The highest increase in oxidized ABTS can be seen at a pH of 5. After 5 hours 15% ABTS are oxidized only through CuCl2. Nevertheless this result does not have an impact on the reactivity of the [http://partsregistry.org/wiki/index.php?title=Part:BBa_K863000 BPUL] laccase at pH 5, which is still the optimal pH. Therefore it has the same pH optimum as TVEL0.
In regard to our project an optimal pH of 5 is a helpful result. Since waste water in waste water treatment plants has a average pH of 6.9 it has to be kept in mind, that a adjustment of the pH is necessary.
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K863000 BPUL] CuCl2 concentration
Another test of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K863000 BPUL] was done to survey the best CuCl2 concentration for the activity of the purified [http://partsregistry.org/wiki/index.php?title=Part:BBa_K863000 BPUL] laccase. 0.03 mg mL-1 of protein were incubated with different CuCl2 concentrations ranging from 0 to 0.7 mM CuCl2. Activity tests were performed with the incubated samples, 0.1 mM ABTS and 100 mM sodium actetate buffer (pH 5) to a final volume of 200 µL. The reactivity was measured at 420 nm, 25°C and over a time period of 5 hours. As expected the saturation takes place after 3 hours (see Figure 12). The differences in the activity of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K863000 BPUL] laccases incubated in different CuCl2 differ minimal. The highest activity of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K863000 BPUL] laccase is observed after incubation with 0.6 mM CuCl2 (52% of added ABTS). With a higher concentration of 0.7 mM CuCl2 the activity seems to be reduced (only 48% ABTS got oxidized). This leads to the assumption that CuCl2 supports the [http://partsregistry.org/wiki/index.php?title=Part:BBa_K863000 BPUL] laccase reactivity but concentrations exceeding this value of CuCl2 may have a negative impact on the ability of oxidizing ABTS. This fits the expectations as laccases are copper reliant enzymes and gain their activity through the incorporation of copper. Additionally negative controls were done using the tested concentrations of CuCl2 without applying laccase to detect the oxidization of ABTS through copper (see Figure 13). The more CuCl2 was present, the more ABTS was oxidzied after 5 hours. Still the maximal change accounts only for ~6% oxidized ABTS after 5 hours.
In relation to apply the laccase in waste water treatment plants it is beneficial knowing, that small amounts of CuCl2 are enough to activate the enzyme. Still it is expensive to be reliant on CuCl2 and a potential risk using heavy metals for waste water purifcation.
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K863000 BPUL] activity at different temperatures
To investigate the activity of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K863000 BPUL] at lower temperatures, activity tests as described above were performed at 10°C and 25°C. A small decrease in the activity can be observed upon reducing the temperature from 25°C to 10°C (see Fig. 14). After 3.5 hours when samples at 25°C reached the saturation samples at 10°C had not, but nonetheless the difference is minimal. After 3 hours 5% difference in oxidized ABTS is observable. The negative control without the [http://partsregistry.org/wiki/index.php?title=Part:BBa_K863000 BPUL] laccase but 0.4 mM CuCl2 at 10°C shows a negligible oxidation of ABTS.
A a decrease in the reactivity of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K863000 BPUL] laccase was expected. The observed small reduction in enzyme activity is excellent news for the possible application in waste water treatment plants where the temperature differs from 8.1°C to 20.8°C.
[http://partsregistry.org/wiki/index.php?title=Part:BBa_K863000 BPUL] activity depending on different ABTS concentrations
Furthermore, [http://partsregistry.org/wiki/index.php?title=Part:BBa_K863000 BPUL] laccase were tested using different amounts of ABTS to calculate KM and Kcat values. The same measurement setup as described above was used only with different amounts of ABTS. As anticipated, the amount of oxidized ABTS increased in dependence of the amount of ABTS used (Figure 15). Especially using 16 µL showed an increase in the activity until 1 hour (reaching 50 µM ABTSox), but the amount of oxidized ABTS decreased afterward.
Impact of MeOH and acteonitrile on [http://partsregistry.org/wiki/index.php?title=Part:BBa_K863000 BPUL]
For substrate analytic tests the influence of MeOH and acetonitrile on [http://partsregistry.org/wiki/index.php?title=Part:BBa_K863000 BPUL] laccases had to be determined, because substrates have to be dissolved in these reagents. The experiment setup included 0.03 mg mL-1 [http://partsregistry.org/wiki/index.php?title=Part:BBa_K863000 BPUL] laccase, different amounts of MeOH (Figure 16) or acteonitrile (Figure 17), 0.1 mM ABTS and 100 mM sodium actetate buffer to a final volume of 200 µL. The observed reactivity of [http://partsregistry.org/wiki/index.php?title=Part:BBa_K863000 BPUL] in regard of oxidizing ABTS did not reveal a huge decrease. The less MeOH or acetonitrile was used, the higher was the amount of oxidized ABTS after 3 hours. An application of 16 µL MeOH or acetonitrile led to a decrease of maximal 10% oxidized ABTS compared to 2 µL MeOH or acetonitrile. Negative controls are shown in Figure 17 and 18 of the ECOL laccase. MeOH and acetonitril are able to oxidize ABTS. After 5 hours at 25°C ~15 µM ABTS get oxidized through MeOH or acetonitrile, but samples with [http://partsregistry.org/wiki/index.php?title=Part:BBa_K863000 BPUL] laccase show a distinct higher activity of 50 µM ABTSox.
Since Regionals: Initial activity tests of purified fractions
After the Regional Jamborees in Amsterdam new cultivations of BPUL started. The most comprising fractions of the purification were analyzed for protein content, re-buffered into deionized H2 and incubated in 0.4 mM CuCl2. Again, the protein content of each fraction was determined because of the loss of proteins through re-buffering. Initial activity tests were done in Britton-Robinson buffer with 0.1 mM ABTS. The protein content of each fraction was adjusted for comparison of the resulting activity (Fig. 10).
Fraction 50% 2 shows the highest activity. The saturation is reached at ~1 h. For comparison it was stated that this fraction contains 90 % laccase and therefor the BPUL concentration is 25,1 µg mL-1.
Since Regionals: [http://partsregistry.org/wiki/index.php?title=Part:BBa_K863000 BPUL] pH optimum
The pH of the medium containing the enzyme is of high importance for its activity. The pH optima of BHAL are pH 4 and pH 5. This is the result of activity measurements using Britton-Robinson buffer with differently adjusted pHs. BHAL laccase was re-buffered into H2 and incubated with 0.4 mM CuCl2. The range from pH 4 to pH 9 was tested under substrate saturation at 25 °C for 30 minutes. At pH 4 and pH 5 ABTS gets oxidized the most fastest (Fig. x). At higher pHs than pH 5, the activity of BPUL is decreased considerably. The resulting Units mg-1 support the observed data (Fig x). irgendwas mit unitszahlen
Since Regionals: [http://partsregistry.org/wiki/index.php?title=Part:BBa_K863000 BPUL] activity depending on different ABTS concentrations
In order to find the substrate saturation, laccase activity was measured with ABTS concentrations ranging from 0.1 mM to 8 mM. 616 ng BPUL laccase were used for measurements with ABTS concentrations of 0.1 mM to 5 mM, 308 ng BPUL laccase were used for measurements with ABTS concentrations of 5 mM to 8 mM. Measurements were done in Britton-Robinson buffer (pH 5) at 25 °C for 30 minutes taking the OD420 every 5 minutes.
Comparing the graphs in Figure x and y, both show a comprising substrate saturation with 5 mM ABTS. Higher concentrations of ABTS than 5 mM do not show any other effects on the activity of BPUL. For all following activity measurements after the Regional Jamborees in Amsterdam a concentration of 5 mM ABTS was applied.
Substrate Analysis
In Figure 18 the degradation reactions of ethinyl estradiole with ABTS of BPUL and ECOL are shown. The data was measured by HPLC. Since it was already determined that both are able to oxidize ABTS by the activity test, the results were as expected. ABTS works as mediator, which explains the ability to degrade ethinyl estradiol and probably other substrates. In comparison, BPUL has a lower potential for degration of ethinyl estradiol with ABTS than TVEL0, but a higher potential than ECOL.
In Figure 19 and 20 the degradation of estradiol by BPUL is shown. BPUL is able to degrade estradiol even without ABTS, but does not has the same potential as the purchased laccase TVEL0.
Immobilization
Figure 20 shows the percentage of laccases in the supernatant 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 show that 75.2% of BPUL remained in the supernatant. This indicates a relatively low binding capacity of BPUL on CPC-beads.
In figure 21, the enzymatic activity of BPUL in the supernatant is compared to the activity of nontreated BPUL. Although an activity can already be detected in the supernatant, this activity is lower compared to the original.
Figure 22 presents the enzymatic activity of immobilized laccases compared to nontreated laccases. The activity of bound BPUL is higher than the activity of ECOL, even if BPUL binds less to the CPC-beads than ECOL.
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