Team:Heidelberg/Delftibactin/Delftibactin

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Delftibactin. Bringing it all together.

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Methods:

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ACM agar plate with D. acidovorans (left) overlaid with 0.2% HAuCl4 in 0.5% agarose

Sequences of movie showing gold precipitation in D. acidovorans supernatant using gold concentrations ranging from 0 to 2.55 µg/ml


29-04 - 05-05-13

Reproduction of Johnsson et al. Paper

Aim

Reproduction of Johnsson et al. paper: Precipitating gold with D.acidovorans on agar plate, in culture, the medium of the culture and possibly purified delftibactin.

Preparations

  • Obtain D. acidovorans from DSMZ
  • Prapare ACM medium as described
  • Prepare ACM agar plates


Gold Precipitation on ACM Plates

  • Culture D. acidovorans for 3 days on agar plates at 30°C
  • Overlay agar plates with 0.2% HAuCl4 in 0.5 % soft agarose

Result

ACM agar plate with D. acidovorans (left) overlaid with 0.2% HAuCl4 in 0.5% agarose

ACM agar plate with D. acidovorans (left) overlaid with 0.2% HAuCl4 in 0.5% agarose

  • Gold precipitation on ACM agar plate worked even better than described in paper


Gold Precipitation in D. acidovorans Supernatants

  • Culture D. acidovorans for 3 days in ACM plates
  • Centrifuge bacteria in liquid culture (10 min 6,000 rpm)
  • Add 0.2% HAuCl4 to supernatant and medium control

Result

D. acidovorans Supernatant (top) and ACM negative control (bottom) with (left to right) 600µl, 400µl, 200µl, 100µl, 50µl, 0µl 0.2% HAuCl4. Far right: top: uncentrifuged solution culture with 600µl 0.2% HAuCl4, bottom: ACM with 600µl HAuCl4

The supernatant/ medium with gold was centrifuged after 2 h reaction time. left to right: supernatant with 600µl 0.2% HAuCl4, ACM with 600µl 0.2% HAuCl4, supernatant with 400µl 0.2% HAuCl4, ACM with 400µl 0.2% HAuCl4, supernatant with 200µl 0.2% HAuCl4, ACM with 200µl 0.2% HAuCl4

  • Gold precipitation with D. acidovorans supernatant worked well


Gold Precipitation in D. acidovorans Supernatants at different Gold Chloride Concentrations

  • Culture D. acidovorans for 3 days in ACM plates
  • Centrifuge bacteria in liquid culture (10 min 6,000 rpm)
  • Add HAuCl4 to supernatant and medium control

Result

Sequences of movie showing gold precipitation in D. acidovorans supernatant using gold concentrations ranging from 0 to 2.55 µg/ml

  • Gold precipitation with supernatant worked at very low concentration Gold
  • Gold precipitation with unpurified culture worked as well

Pins removed from an old CPU.

Green solution of dissolved pins.

Gold chloride solution obtained from an old CPU.

Solid gold precipitated by D. acidovorans.


13-05 - 19-05-13

Gold Recovery from Electronic Waste

As test experiment, pins from an old CPU processor chip were dissolved.

Fig.0 Old motherboard from which we will recycle gold.


Step 1: Pins were mechanically removed and collected in a flask.

Fig.1.1 CPU from which pins will be removed.

Fig.1.2 Removed pins.

Step 2: Flask was put onto heating plate and covered in concentrated HCl.

Fig.2 Pins covered in HCl.

Step 3: HNO3 was carefully added to the pins and heated.

Fig.3 Evolution NO2 gas.

Step 4: After several minutes of moderate heating, pins dissolved completely. The solution turned green.

Fig.4 Green solution of dissolved pins.

Step 5: The solution was carefully neutralized to pH ~6 in a step-wise manner using first 5 M, later 0.5 M NaOH.
Step 6: This led to precipitation of copper salts, indicated by the milky green coloring.

Fig.6 Milky solution following neutralization.

Step 7: In order to remove the precipitates, the solution was filtered using a buechner funnel and sterile filtrated (0.2 µm).

Fig.7.1 Filtering solution to remove precipitates.

Fig.7.2 Sterile filtering.

Fig.7.3 Filters used for sterile filteration.

Step 8: The final yellow-green gold containing solution was collected in a volumetric flask.

Fig.8Final gold containing solution.


Precipitation of Gold from Electronic Waste

Protocol

In order to evaluate optimial cultivation temperature of D. acidovorans, glycerol stock was streaked on ACM plates and incubated at RT, 30°C and 37°C ON. The next day, plates were covered with 200 µl 0.5% soft agar supplemented with 27 µl "dissolved electronic waste" solution.

Result

D. acidovorans showed intermediate, postponed purple-black coloring upon addition of "dissolved electronic waste" soft agar. Strongest coloring was observed on plates incubated at room temperature and 30°C. Delftibactin expression seems to be significantly decreased in D. acidovorans cultivated at 37°C. Reduced coloring further indicates lower gold ion concentration in the solution recovered compared to th ecommercially availible gold chloride solution [100 g/l]
We could therefore prove capability of D. acidovorans to specifically recover solid gold from dissolved electronic waste.

Fig.9.1 "Dissolved electronic waste" and D. acidovorans.

Fig.9.2 ACM plates prior to addition of gold chloride solution.

Fig.9.3 ACM plates covered with gold chloride solution T= 0:00 h.

Left plate: RT, upper plate: 30°C, lower right plate: 37°C

Fig.9.4 ACM plates covered with gold chloride solution T= 0:30 h.

Fig.9.5 ACM plates covered with gold chloride solution T= 1:00 h.

Fig.9.6 ACM plates covered with gold chloride solution T= 1:30 h.

Sparkling gold appearing in the melting pot.

Final recovered solid gold collected in tube.

Solid gold recovered from nanoparticles in 2 ml tube.

05-08 - 11-08-13

Melting Gold Nanoparticles to Solid Gold

Step 1: Cultivation of D. acidovorans
200 ml ACM medium were inocculated with recently obtained D. acidovorans SPH-1 from glycerol stock and incubated at 30°C for 3 days.

Step 2: Precipitation of Gold Nanoparticles

  • D. acidovorans culture in ACM was divided in 50 ml aliquots and centrifuges at 3,750 rpm for 30 min.
  • Supernatant was transferred to fresh tube.
  • 300 µl gold chloride stock solution [µg/ml] was added to D. acidovorans supernatant, suspention mixed and incubated at RT for 20 min.

Fig.2.1 Supernatant of D. acidovorans.

Fig.2.2 Precipitated gold nanoparticles in D. acidovorans supernatant.


Step 3: Aggregation of gold nanoparticles.

Fig.3 Gold nanoparticle solution on melting pot.

Step 4: Melting gold nanoparticles to solid gold.

Fig.4.1 Heating aggregated gold nanoparticles in melting pot.

Fig.4.2 Heating aggregated gold nanoparticles in melting pot upside down.

Fig.4.3 Remaining solid gold in melting pot.

Fig.4.3 Sparkling gold appearing in the melting pot.

Fig.4.4 Final recovered solid gold collected in tube.



Alternatively, we also performed the protocol described above in a 2 ml tube.

Fig.5 Solid gold recovered from nanoparticles in 2 ml tube.


02-09 - 08-09-13

Optimizing Growth Conditions of D.acidovorans and Evaluation of Endogenous Background Gold Precipitation

In order to optimize plates for cultivation of D.acidovorans as well as to evaluate of endogenous capability of possible target strains, capability of D.acidovorans and E. coli DH10ß and BL21 DE3 grown on LB and ACM plates was tested.

On Agar Plate following ON Incubation at 30°C

  • On agar plates, D.acidovorans, E.coli DH10ß, and Bl21 were plated from liquid culture and grown ON at 30 °C.
  • The following day, 1.6 ml soft agar (0.5%) was mixed with goldchloride [100 g/l] as follows:
Final goldchloride
concentration [mM] 		Volume goldchloride
stock [µl]
5 27
10 54.4
20 108.8
Agar plate Goldchloride [mM] H2O D.acidovorans DH10ß BL21 DE3
ACM 0 no reaction no reaction no reaction no reaction
ACM 5 postponed weak coloring ON weak coloring after 2 min weak coloring after 2 min weak coloring after 2 min
ACM 10 postponed dark coloring ON strong coloring after 2 min strong coloring after 2 min strong coloring after 2 min
ACM 20 postponed dark coloring ON strong coloring after 2 min strong coloring after 2 min strong coloring after 2 min
LB 0 no reaction no reaction no reaction no reaction
LB 5 no reaction no reaction no reaction no reaction
LB 10 no reaction no reaction no reaction no reaction
LB 20 no reaction no reaction no reaction no reaction

Result

Evaluation of Bacteria regarding Background Gold Precipitation on Agar Plate following ON Incubation at 30°C

ACM plate before incubation with gold chloride containing soft agar.

ACM plate after incubation with gold chloride containing soft agar counter-clockwise beginning from top left in concentrations of 0 mM, 5 mM, 10 mM, 20 mM.

All bacteria showed strong and immediate purple-black coloring indicating gold precipitation depending on gold chloride concentration. Regarding the precipitation of gold, there does not seem to be a significant advantage of D.acidivorans. In contrast to the paper from Johnston et al., we only grew them ON at 30°C rather than for 3 days. We will repeat the experiment using 3 day incubation time and also evaluate gold precipitation on additional media as well as by additional bacteria.


Test if purified Delftibactin is able to precipitate gold. From left to right: ACM media, filtered supernatant D. acidovorans, purified Delftibactin

Test if purified Delftibactin (diluted 1:10 in H2O) is able to precipitate gold. From left to right: water, 1:10 ACM media, 1:10 supernatant D. acidovorans, 1:10 filtered supernatant D. acidovorans, 1:10 purified Delftibactin

09-09 - 15-09-13

Optimizing Growth Conditions of D.acidovorans and Evaluation of Endogenous Background Gold Precipitation

In order to optimize plates, growth time and incubation temperature of D.acidovorans as well as to evaluate of endogenous capability of possible target strains, various growth conditions and bacteria were tested.

On Agar Plate following 3 Day Incubation at 30°C

  • Media was chelex treated, agar added and autoclaved, before plates were poured.
  • On agar plates, D.acidovorans, E.coli DH10ß, Bl21 DE3, and BL21 pLys as well as MG1655 and Bacillus subtilus were plated from liquid culture and grown for three days at 30 °C.
  • 14.4 ml soft agar (0.5%) was mixed with gold chloride [100 g/l] as follows and 200 µl per quarter plate added:
Final gold chloride
concentration [mM] 		Volume goldchloride
stock [µl]
0 0
0.5 2.7
2.5 13.5
5 27

Result

Agar plate Goldchloride [mM] H2O D.acidovorans BL21 DE3 BL21 pLys H2O DH10ß B.circulans MG1655
ACM 0 no reaction no reaction no reaction no reaction no reaction no reaction no reaction no reaction
ACM 0.5 no reaction no reaction no reaction no reaction no reaction no reaction no reaction no reaction
ACM 2.5 minor coloring minor coloring no reaction no reaction no reaction no reaction minor coloring no reaction
ACM 5 strong coloring strong coloring intermediate coloring minor coloring minor coloring minor coloring minor coloring minor coloring
LB 0 no reaction no reaction no reaction no reaction no reaction no reaction no reaction no reaction
LB 0.5 no reaction no reaction no reaction no reaction no reaction no reaction no reaction no reaction
LB 2.5 no reaction no reaction no reaction no reaction no reaction no reaction no reaction no reaction
LB 5 no reaction no reaction no reaction no reaction no reaction no reaction no reaction no reaction
M9 0 no reaction no reaction no reaction no reaction no reaction no reaction no reaction no reaction
M9 0.5 minor coloring no reaction no reaction no reaction no reaction no reaction no reaction no reaction
M9 2.5 strong coloring minor coloring no reaction no reaction strong coloring minor coloring strong coloring no reaction
M9 5 strong coloring minor coloring no reaction no reaction minor coloring minor coloring minor coloring no reaction
Gold precipitation on ACM plates incubated for 3 days at 30°C

Fig.1.1 Gold precipitation on ACM plates incubated for 3 days at 30°C: prior to addition of soft agar.

Fig.1.2 Gold precipitation on ACM plates incubated for 3 days at 30°C: T= 0:00.

Fig.1.3 Gold precipitation on ACM plates incubated for 3 days at 30°C: T= 0:20.

Fig.1.4 Gold precipitation on ACM plates incubated for 3 days at 30°C: T= 0:50.

Fig.1.5 Gold precipitation on ACM plates incubated for 3 days at 30°C: T= 1:00.

Fig.1.6 Gold precipitation on ACM plates incubated for 3 days at 30°C: T= 2:00.

Fig.1.7 Gold precipitation on ACM plates incubated for 3 days at 30°C: T= 3:00.

Gold precipitation on LB plates incubated for 3 days at 30°C

Fig.2.1 Gold precipitation on LB plates incubated for 3 days at 30°C: T= 0:00.

Fig.2.2 Gold precipitation on LB plates incubated for 3 days at 30°C: T= 0:10.

Fig.2.3 Gold precipitation on LB plates incubated for 3 days at 30°C: T= 0:20.

Fig.2.4 Gold precipitation on LB plates incubated for 3 days at 30°C: T= 0:50.

Fig.2.5 Gold precipitation on LB plates incubated for 3 days at 30°C: T= 2:00.

Gold precipitation on M9 plates incubated for 3 days at 30°C

Fig.3.1 Gold precipitation on M9 plates incubated for 3 days at 30°C: T= 0:00.

Fig.3.2 Gold precipitation on M9 plates incubated for 3 days at 30°C: T= 0:10.

Fig.3.3 Gold precipitation on M9 plates incubated for 3 days at 30°C: T= 0:20.

Fig.3.4 Gold precipitation on M9 plates incubated for 3 days at 30°C: T= 0:50.

Fig.3.5 Gold precipitation on M9 plates incubated for 3 days at 30°C: T= 2:00.

Unfortunately, the streaked E.coli DH10ß were contaminated (obvious only on LB plates) and can threfore not be analyzed.
On ACM plates following 30°C incubation, D.acidovorans, B.circulans, E.coli BL21 DE3 as well as the negative control next to D.acidovorans, but not the one on plate B, showed immediate purple-black coloring indicating formation of gold nanoparticles at 5 mM gold chloride. At 2.5 mM, D.acidovorans and the neighbouring negative control as well as B.circulans showed some coloring. E.coli BL21 pLys and MG1655 only showed minor coloring at 5 mM. At lower concentrations, no gold precipitation was observed.

=> E.coli BL21 pLys and MG1655 are promissing candidates for expression since they show the least background activity.
=> Optimal gold chloride concentration lies between 2.5 and 5 mM.
=> Delftibactin can diffuse through agar.


On LB plates following 30°C incubation, none of the tested bacteria showed any reaction.

=> LB is not suitable for expression of NRPs.
=> What is missing in LB that does not allow metall precipitating activity?


On M9 plates following 30°C incubation (which were mistakenly autoclaved after addition of glucose), D.acidovorans hardly grew. At 5 mM and 2.5 mM gold chloride, there is heavy background activity on the negative controls. Additionally, B.circulans shows strong - D.acidovorans minor formation of nanoparticles.

=> M9 is not suitable for gold precipitation experiments.


On Agar Plate following 3 Day Incubation at RT

  • Media was chelex treated, agar added and autoclaved, before plates were poured.
  • On agar plates, D.acidovorans, E.coli DH10ß, Bl21 DE3, and BL21 pLys as well as MG1655 and Bacillus subtilus were plated from liquid culture and grown for three days at RT.
  • 14.4 ml soft agar (0.5%) was mixed with gold chloride [100 g/l] as follows and 200 µl per quarter plate added:
Final gold chloride
concentration [mM] 		Volume goldchloride
stock [µl]
0 0
0.5 2.7
2.5 13.5
5 27

Result

Agar plate Goldchloride [mM] H2O D.acidovorans BL21 DE3 BL21 pLys H2O DH10ß B.circulans MG1655
ACM 0 no reaction no reaction no reaction no reaction no reaction no reaction no reaction no reaction
ACM 0.5 no reaction no reaction no reaction no reaction no reaction no reaction no reaction no reaction
ACM 2.5 no reaction no reaction no reaction no reaction minor coloring minor coloring intermediate coloring minor coloring
ACM 5 strong coloring strong coloring minor coloring minor coloring intermediate coloring strong coloring strong coloring strong coloring
LB 5 no reaction no reaction no reaction no reaction no reaction no reaction no reaction no reaction
M9 5 strong coloring strong coloring no reaction no reaction strong coloring strong coloring strong coloring no reaction
Gold precipitation on ACM plates incubated for 3 days at RT

Fig.4.1 Gold precipitation on ACM plates incubated for 3 days at RT: T= 0:00.

Fig.4.2 Gold precipitation on ACM plates incubated for 3 days at RT: T= 0:10.

Fig.4.3 Gold precipitation on ACM plates incubated for 3 days at RT: T= 0:20.

Fig.4.4 Gold precipitation on ACM plates incubated for 3 days at RT: T= 1:00.

Gold precipitation on LB plates incubated for 3 days at RT

Fig.5.1 Gold precipitation on LB plates incubated for 3 days at RT: T= 0:00.

Fig.5.2 Gold precipitation on LB plates incubated for 3 days at RT: T= 0:10.

Fig.5.3 Gold precipitation on LB plates incubated for 3 days at RT: T= 0:20.

Fig.5.4 Gold precipitation on LB plates incubated for 3 days at RT: T= 1:00.

Gold precipitation on M9 plates incubated for 3 days at RT

Fig.6.1 Gold precipitation on M9 plates incubated for 3 days at RT: T= 0:00.

Fig.6.2 Gold precipitation on M9 plates incubated for 3 days at RT: T= 0:10.

Fig.6.3 Gold precipitation on M9 plates incubated for 3 days at RT: T= 0:20.

Fig.6.4 Gold precipitation on M9 plates incubated for 3 days at RT: T= 1:00.


On ACM plates following RT incubation, D.acidovorans and the neighbouring negative control, B.circulans and E.coli MG1655 show minor immediate coloring at 5 mM. At lower concentrations, no activity can be observed.

=> There is less Delftibactin expression in D.acidovorans at lower temperatures.
=> E.coli BL21 pLys remains a promissing candidate for expression since they show the least background activity.


On LB plates following RT incubation, there is again nothing to see.

On M9 plates following RT incubation, there is again high background at negative controls as well as intermediate coloring for D.acidovorans and B.circulans.
We will therefore analyze gold precipitation capacities of supernatants of D.acidovorans, E.coli DH10ß, BL21 DE3, BL21 pLys and MG1655 in ACM liquid medium following 48 and 72 h.

In ACM Medium following 2 Day Incubation at 30°C

  • In 5 ml ACM medium, D.acidovorans, E.coli DH10ß, Bl21 DE3, and BL21 pLys as well as MG1655 and pure medium were inocculated and grown for two days at 30°C.
  • 1 ml supernatant was mixed with gold chloride [100 g/l] as follows:
Final gold chloride
concentration [µg/ml] 		Volume goldchloride
stock [µl]
0.6 6

Result

Following addition of gold chloride solution, E.coli DH10ß, Bl21 DE3, and BL21 pLys showed rapid purple-black coloring indicating gold nanoparticle formation. They exceed the capacity of D.acidovorans, which showed gold precipitation slightly faster than E.coli MG1655. The ACM did not show any background activity.
We will extend the incubation time of the cultures further to evaluate differences, possibly due to accumulation of Delftibactin in the medium.

Evaluation of Bacteria regarding Background Gold Precipitation in ACM liquid Medium following 2 day Incubation at 30°C

Fig.1.1 From left: 1 ml ACM medium, supernatants of E.coli DH10ß, MG1655, Bl21 pLys and BL21 DE3 as well as D.acidovorans and 6 µl gold chloride stock solution in lid.

Fig.1.2 From left: 1 ml ACM medium, supernatants of E.coli DH10ß, MG1655, Bl21 pLys and BL21 DE3 as well as D.acidovorans prior to mixing.

Fig.1.3 From left: 1 ml ACM medium, supernatants of E.coli DH10ß, MG1655, Bl21 pLys and BL21 DE3 as well as D.acidovorans: T= 0:00 s. Particles on to bottom are undissolved gold chloride.

Fig.1.4 From left: 1 ml ACM medium, supernatants of E.coli DH10ß, MG1655, Bl21 pLys and BL21 DE3 as well as D.acidovorans: T= 30 s.

Fig.1.5 From left: 1 ml ACM medium, supernatants of E.coli DH10ß, MG1655, Bl21 pLys and BL21 DE3 as well as D.acidovorans: T= 1:00 min.

Fig.1.6 From left: 1 ml ACM medium, supernatants of E.coli DH10ß, MG1655, Bl21 pLys and BL21 DE3 as well as D.acidovorans: T= 2:00 min.

Fig.1.7 From left: 1 ml ACM medium, supernatants of E.coli DH10ß, MG1655, Bl21 pLys and BL21 DE3 as well as D.acidovorans: T= 3:00 min.

Fig.1.8 From left: 1 ml ACM medium, supernatants of E.coli DH10ß, MG1655, Bl21 pLys and BL21 DE3 as well as D.acidovorans: T= 4:00 min.

Fig.1.9 From left: 1 ml ACM medium, supernatants of E.coli DH10ß, MG1655, Bl21 pLys and BL21 DE3 as well as D.acidovorans: T= 5:00 min.



In ACM Medium following 3 day Incubation at 30°C

  • In 5 ml ACM medium, D.acidovorans, E.coli DH10ß, Bl21 DE3, and BL21 pLys as well as MG1655 were inocculated and grown for three days at 30°C.
  • 1 ml supernatant was mixed with gold chloride [100 g/l] as follows:
Final gold chloride
concentration [µg/ml] 		Volume goldchloride
stock [µl]
0.6 6

Result

Again, E. coli DH10ß, Bl21 DE3, and BL21 pLys showed rapid purple-black coloring exceeding the capacity of D.acidovorans and E. coli MG1655. These results are highly inconclusive and the experiment has to be repeated.

Evaluation of Bacteria regarding Background Gold Precipitation in ACM liquid Medium following 3 day Incubation at 30°C

Fig.1.1 From left: 1 ml ACM medium, supernatants of E.coli DH10ß, MG1655, Bl21 pLys and BL21 DE3 as well as D.acidovorans and 6 µl gold chloride stock solution in lid.

Fig.1.2 From left: 1 ml ACM medium, supernatants of E.coli DH10ß, MG1655, Bl21 pLys and BL21 DE3 as well as D.acidovorans prior to mixing.

Fig.1.3 From left: 1 ml ACM medium, supernatants of E.coli DH10ß, MG1655, Bl21 pLys and BL21 DE3 as well as D.acidovorans: T= 0:00 min. Particles on to bottom are undissolved gold chloride.

Fig.1.4 From left: 1 ml ACM medium, supernatants of E.coli DH10ß, MG1655, Bl21 pLys and BL21 DE3 as well as D.acidovorans: T= 1:00 min.

Fig.1.5 From left: 1 ml ACM medium, supernatants of E.coli DH10ß, MG1655, Bl21 pLys and BL21 DE3 as well as D.acidovorans: T= 2:00 min.

Fig.1.6 From left: 1 ml ACM medium, supernatants of E.coli DH10ß, MG1655, Bl21 pLys and BL21 DE3 as well as D.acidovorans: T= 5:00 min.

Fig.1.7 From left: 1 ml ACM medium, supernatants of E.coli DH10ß, MG1655, Bl21 pLys and BL21 DE3 as well as D.acidovorans: T= 6:00 min.

Fig.1.8 From left: 1 ml ACM medium, supernatants of E.coli DH10ß, MG1655, Bl21 pLys and BL21 DE3 as well as D.acidovorans: T= 7:00 min.

Fig.1.9 From left: 1 ml ACM medium, supernatants of E.coli DH10ß, MG1655, Bl21 pLys and BL21 DE3 as well as D.acidovorans: T= 10:00 min.

Fig.1.10 From left: 1 ml ACM medium, supernatants of E.coli DH10ß, MG1655, Bl21 pLys and BL21 DE3 as well as D.acidovorans: T= 13:00 min.

Fig.1.11 From left: 1 ml ACM medium, supernatants of E.coli DH10ß, MG1655, Bl21 pLys and BL21 DE3 as well as D.acidovorans: T= 15:00 min.


Purification of Delftibactin

Purification

  • Grew 1 L of D. acidovorans SPH1 for 24h in ACM media at 30°C. (2x 500 mL ACM 15 mL about 3 days old D. acidovorans culture in ACM)
  • Centrifugation of culture at 3750 rpm for 30 min
  • Retrieved supernatant
  • Added 20 g/L HP-20
  • Stirred at RT for 2 h
  • Filtration with Buchner funnel to retain HP-20
  • Washed with 400 ml dddH2O
  • Elution with 400 ml Methanol
  • Evaporated methanol with rotary evaporator
  • Resuspended in 2 ml 50 methanol : 50 ddH2O


Testing Purified Delftibactin

Different intermediate products were tested for their ability to precipitate gold. For this, 3 µl of AuCl3 (100g/l) were added to 500 µl solution. The outcome is presented in the following table.

Sample Precipitating Gold? Colour of Precipitate Time until Precipitation Started
AMC media yes grey ~2 h
Supernatant of D. acidovorans SPH-1 culture yes black 1:30 min
Supernatant after treatment with HP20 yes black 1:40 min
HP20 after elution step no -- --
Methanol no -- --
Methanol used for elution no -- --


Sample Diluted in Water Volume sample Gold Solution 100g/l Precipitating gold? Colour of Precipitate Time until Precipitation Started
ACM media -- 160 µl 1 µl yes black 1 h
Supernatant of D. acidovorans in ACM, filtered -- 160 µl 1 µl yes black 1 h
Purified Delftibactin after dilution in 50:50 Methanol, Water -- 160 µl 1 µl no -- --
Water -- 250 µl 1.5 µl no -- --
ACM media 1:10 250 µl 1.5 µl no -- --
Supernatant of D. acidovorans in ACM 1:10 250 µl 1.5 µl no -- --
Supernatant of D. acidovorans in ACM, filtered 1:10 250 µl 1.5 µl no -- --
Purified Delftibactin after dilution in 50:50 Methanol, H2O 1:10 250 µl 1.5 µl yes gray over night
Testing Purified Delftibactin for Capability to Precipitate Gold

Test if purified Delftibactin is able to precipitate gold. From left to right: ACM media, filtered supernatant D. acidovorans, purified Delftibactin

Test if purified Delftibactin (diluted 1:10 in H2O) is able to precipitate gold. From left to right: water, 1:10 ACM media, 1:10 supernatant D. acidovorans, 1:10 filtered supernatant D. acidovorans, 1:10 purified Delftibactin

Micro-TOF

The supernatant of a 24 h D. acidovorans SPH-1 culture was analysed before and after the purification procedure using a MICRO-TOF. As negative control unpurified ACM media was measured as well.
File:Heidelberg 20130911Malditof.pdf

Result

Delftibactin was clearly present in the purified supernatant of the D. acidovorans SPH-1 culture. In contrast it could not be detected in the ACM media or the supernatant which was not purified.

Triple Clone pIK8.6, DelH and DelH I 6B

Preparations

Electrocompetent E. coli DH10ß and BL21 DE3 were prepared as described.

Electroporation

We electroporated all three plasmids into E. coli DH10ß using pIK8.6. Although the DelH clone I 6B has a deletion in the ribosome binding site, we hope that we still get enough expression of DelH.

Electroporation Total amount of DNA [ng] Ratio pIK2.6:
DelH:DelRest 		pIK8.6-1(12 Kb, 146 ng/µl) DelH-I6B midi (23 Kb, 235.2 ng/µl) DelRest (32 Kb, 2.4 µg/µl)
Triple into E. coli DH10ß 774.2 1:2:3 1 µl of 1:10 (146 ng) 1 µl (235.2 ng) 1.5 µl of 1:10 (375 ng)

Preparation of Cultures for Purification and MICRO-TOF

Bacteria Media Antibiotics
-- ACM --
E. coli DH10ß ACM --
Delftia acidovorans SPH-1 ACM --
E. coli DH10ß with plasmids pHM04 (I6B), pFSN (D8w) & pIK8.6 ACM Ampicillin, Chloramphenicol, Kanamycin
  • Inoculation of 10 ml of over night cultures of each sample
  • Growth at 30°C (Delftia acidovorans) and 37°C (E. coli DH10ß and E. coli DH10ß + plasmids pHM04 (I6B), pFSN (D8w) & pIK8.6)
  • For each culture, 500 ml of ACM media with antibiotics was inoculated with the pre-cultures
  • The cultures were grown for about 8 h.

ODs

  • E. coli DH10ß = 1.2
  • Delftia acidovorans SPH-1 = 0.4
  • E. coli DH10ß + plasmids pHM04 (I6B), pFSN (D8w) & pIK8.6 = 0.8


Purification of Delftibactin

  • Centrifugation of cultures at 3750 rpm for 30 min
  • Retrieved supernatant
  • Added 20 g/L HP-20
  • Stirred at RT for 2 h
  • Filtration with Buchner funnel to retain HP-20
  • Washed with 400 ml dddH2O
  • Elution with 200 ml Methanol
  • Evaporated methanol with rotary evaporator
  • Resuspended in 2 ml 50 methanol : 50 ddH2O


MICRO-TOF

File:Heidelberg Microtof0913.pdf

Result

Apparently the purification of delftibactin did not work, as even in the positive control (D. acidovorans SPH-1) no delftibactin was detected. As the cultures were harvested after only a short time of growth it is suspected that maybe the production of delftibactin had not started yet. The next time the cultures should grow for longer.

17-09 - 22-09-13

Triple Clone pIK2.6, DelH and DelH I 6B

Electroporation

We electroporated all three plasmids again into E. coli BL21 DE3. This time, we incubated them them for 3 full days.

Electroporation Total amount of DNA [ng] Ratio pIK8.6:
DelH:DelRest 		pIK8.6-1(12 Kb) DelH-I6B midi (23 Kb, 235.2 ng/µl) DelRest (32 Kb, 2.4 µg/µl)
Triple into E. coli DH10ß 774.2 1:2:3 1 µl of 1:10 (146 ng) 1 µl (235.2 ng) 1.5 µl of 1:10 (375 ng)

Preparation of Cultures for Purification and MICRO-TOF

Bacteria Media Antibiotics
-- ACM --
Delftia acidovorans SPH-1 ACM Ampicillin
E. coli BL21 DE3 ACM --
E. coli BL21 DE3 with plasmids pHM04 (I6B), pFSN (D8w) & pIK8.6 ACM Ampicillin, Chloramphenicol, Kanamycin
  • Inoculation of 10 ml of over night cultures of each sample
  • For DH10β with plasmids pHM04 (I6B), pFSN (D8w) & pIK8.6 no such culture was made
  • Growth at 30°C
  • For each culture 1 L of ACM media with antibiotics was inoculated with this pre-culture
  • 1 L of ACM media with antibiotics was directly inoculated with 1 mL of a 3 hour culture DH10β with plasmids pHM04 (I6B), pFSN (D8w) & pIK8.6 which had originally been made from a clone which had been picked from the agar plate. The 1 L culture was started 3 hours later than the other cultures
  • Expression was induced in E. coli BL21 DE3 with 1 mM IPTG after 8 h of growth
  • Cultures were harvested after 64 hours of growth

Purification of Delftibactin

  • Centrifugation of cultures at 3750 rpm for 30 min
  • Retrieved supernatant
  • Added 20 g/L HP-20
  • Stirred at RT for 2 h
  • Filtration with Buchner funnel to retain HP-20
  • Washed with 400 ml dddH2O
  • Elution with 400 ml Methanol
  • Evaporated methanol with rotary evaporator
  • Resuspended in 2 ml 50 methanol : 50 ddH2O

MICRO-TOF

File:Heidelberg Microtof0925.pdf

Result

Only in the culture of D. acidovorans SPH-1 Delftibactin could be detected. The samples were negative for delftibactin. Apparently our triple clone does not produce delftibactin. However, this is not surprising, since the DelH clone I 6B harbors a mutation in the promoter region.


mRPF Expression in E. coli BL21 DE3, DH10ß and NEB Turbo 16 h post iduction.

mRPF Expression in E. coli BL21 DE3, DH10ß and NEB Turbo 16 h post iduction in liquid media.


23-09 - 29-09-13

Evaluation of Background Expression and Indcibility of Possible Target Strains

Electroporation of mRFP Controls

1 µl miniprpep DNA of the backbones pSB6A1 and pSB3C5 containing mRFP were elctroporated in E.coli Bl21 DE3. Cells were streaked on LB Amp + Chlor plates and stored at RT for two days.

Result

All plates were heavily overgrown. As discussed next, the obtained BL21 DE3 were actually BL21 DE3 pLys and therefore resitant to chloramphenicol. Electroporation has to be repeated, after real E. coli BL21 DE3 are obtained.

New BL21 DE3

We obtained new BL21 DE3 from the Russel Lab, which were obtained from NEB directly. Cells were inocculated in 10 ml LB and streaked on LB Chlor plates. The vial was frozen again at -80°C.

Electroporation of mRFP Controls

Real E. coli BL21 DE3, DH10ß and NEB Turbo were co-electroporated with 1 µl miniprpep DNA of the backbones pSB6A1 and pSB3C5 containing mRFP to check for leaky ecpression. Transformed bacteria were streaked on 2YT plates with Amp + Chlor and incubated ON at 30°C.
The next day, expression of mRFP on backbones pSB6A1 and pSB3C5 was induced by 50 µl 1 mM IPTG as well as inocculated in YT Amp + Chlor + 1 mM IPTG.

Result

After 6 h, only BL21 DE showed expression of mRFP. Yet, it was not restricted to the induced area. Another 10 h later, all strains showed red colonies with and without induction. E. coli BL21 DE3 showed least background expression and intermediate expression upon induction on plate and in liquid media.

mRPF Expression in BL21 DE3, DH10ß and NEB Turbo with and without Induction

Fig.1.1 mRPF Expression in E. coli BL21 DE3 6 h post iduction.

Fig.1.2 mRPF Expression in E. coli BL21 DE3 6 h post iduction.

Fig.1.3 mRPF Expression in E. coli DH10ß 6 h post iduction.

Fig.1.4 mRPF Expression in E. coli NEB Turbo 6 h post iduction.

Fig.1.5 mRPF Expression in E. coli NEB Turbo 6 h post iduction.

Fig.1.6 mRPF Expression in E. coli BL21 DE3, DH10ß and NEB Turbo 16 h post iduction.

Fig.1.7 mRPF Expression in E. coli BL21 DE3, DH10ß and NEB Turbo 16 h post iduction in liquid media.


Electrocompetent E. coli BL21 DE + DelRest and pIK8.6

Electroporation of DelRest, DelH and pIK8.6

As stated above, BL21 DE3 showed least background expression of mRFP and were therefore chosen for preparation of electrocompetent cells as described. Cells were streaked on 2YT Kan + Chlor plates and incubated at RT for 2 days.

Colony-PCR Conditions CP.W22.A

6 colonies were analyzed for Del Rest and pIK8.6 by colony PCR.

  • DelL
Reagent Amount [µl]
Colonies -
FS_14 10 µM 1
FS_15 10 µM 1
OneTaq Master Mix 10
DMSO 1
ddH2O 7
Cycles Temperature [°C] Time [s]
1 95 300
12 95 30
66 ↓ 0.5 30
72 90
18 95 30
63 30
72 90
1 72 720
1 12 inf
  • pIK8.6
Reagent Amount [µl]
Colonies -
VF2 10 µM 1
IK_25 10 µM 1
OneTaq Master Mix 10
DMSO 1
ddH2O 7
Cycles Temperature [°C] Time [s]
1 95 300
35 95 30
54 30
72 90
1 72 600
1 12 inf

Result

Expected band: ~1.4 Kb (DelL) and ~1 Kb (pIK8.6)

Fig22.2 Screening of DelRest + pIK8.6 Co-transformants

All of the analyzed colonies shows expected band for DelL.

=> Inocculate 2 ml 2YT Kan + Chlor with 2 colonies for preparation of electrocompetent cells


Electrocompetent Cells

Electrocompetent E. coli BL21 DE3 + DelRest + pIK8.6 wer prepared as described.

30-09 - 06-10-13

Triple Clone pIK.6, DelRest and DelH C5

Electroporation

E. coli BL21 DE3 + DelRest + pIK8.6 were electroporated with DelH C5 miniprep DNA and streaked on 2YT + Amp + Chlor + Kan plates and incubated at RT for 2 days.

Evaluation of Gold Precipitation on ACM Plates

In order to evaluate gold nanoparticle formation capacity DelH clone C5 in presence of DelRest and pIK8.6, they were streaked on ACM plates as follows and incubated at 30°C for 3 days. As controls, we used the BL21 DE3 transformed with pSB3C5 and pSB6A1.

Plate Antibiotic Cells
ACM - D.acidovorans
E.coli BL21 DE3 + pSB3C5 + pSB6A1
E.coli BL21 DE3 + DelH C5 + DelRest + pIK8.6
empty
ACM Amp + Chlor + Kan D.acidovorans
E.coli BL21 DE3 + pSB3C5 + pSB6A1
E.coli BL21 DE3 + DelH C5 + DelRest + pIK8.6
empty
ACM + IPTG Amp + Chlor + Kan D.acidovorans
E.coli BL21 DE3 + pSB3C5 + pSB6A1
E.coli BL21 DE3 + DelH C5 + DelRest + pIK8.6
empty

Following 3 day incubation, 200 µl 5 mM gold chloride in soft agar was applied.

Result

Evaluation of Gold Precipitation of C5 Triple Clone on ACM Plates following 3 day Incubation at 30°C

Fig.1.1 From left: background control, E.coli BL21 DE3 containing ampicillin and chloramphenicol parts, E.coli BL21 DE3 containing DelH C5, DelRest and pIK8.6 and D.acidovorans prior to addition of gold chloride soft agar.

Fig.1.2 rom left: background control, E.coli BL21 DE3 containing ampicillin and chloramphenicol parts, E.coli BL21 DE3 containing DelH C5, DelRest and pIK8.6 and D.acidovorans: T= 0:00.

Fig.1.3 rom left: background control, E.coli BL21 DE3 containing ampicillin and chloramphenicol parts, E.coli BL21 DE3 containing DelH C5, DelRest and pIK8.6 and D.acidovorans: T= 0:15.

Fig.1.4 rom left: background control, E.coli BL21 DE3 containing ampicillin and chloramphenicol parts, E.coli BL21 DE3 containing DelH C5, DelRest and pIK8.6 and D.acidovorans: T= 0:30.

Fig.1.5 rom left: background control, E.coli BL21 DE3 containing ampicillin and chloramphenicol parts, E.coli BL21 DE3 containing DelH C5, DelRest and pIK8.6 and D.acidovorans: T= 1:00.

Fig.1.6 rom left: background control, E.coli BL21 DE3 containing ampicillin and chloramphenicol parts, E.coli BL21 DE3 containing DelH C5, DelRest and pIK8.6 and D.acidovorans: T= 1:30.

Unexpectedly, the D.acidovorans control grew on the ACM + Amp + Chlor + Kan plates, indicating a contamination with triple resistant bacteria. Therefore, the experiment is inconclusive and has to be repeated. Moreover, the background control shows significant activity.
Nevertheless, there was neither increased activity of the induced 'E.coli BL21 DE3 containing DelH C5, DelRest and pIK8.6 compared to the E.coli BL21 DE3 negative control nor to the not induced control.

Preparation of Cultures for Purification and MICRO-TOF

Bacteria Media Antibiotics
E. coli BL21 DE3 ACM --
Delftia acidovorans SPH-1 ACM --
E. coli BL21 DE3 with plasmids pHM04 (C5), pFSN (D8w) & pIK8.6 ACM Ampicillin, Chloramphenicol, Kanamycin
  • Inoculation of 10 ml of over night cultures of each sample
  • Growth at 30°C
  • For each culture, 1 L of ACM media with antibiotics was inoculated with the pre-culture
  • Expression was induced in all E. coli BL21 DE3 with 1 mM IPTG after 24 h of growth
  • All cultures were supplemented with 10 mM sodium propionate after 24 h of growth
  • The cultures selected with ampicillin were supplemented with an additional 1:2000 ampicillin after 24 h of growth
  • Cultures were harvested after 48 hours of growth and 24 hours after induction

Purification of Delftibactin

  • Centrifugation of cultures at 3750 rpm for 45 min

Protocol for liquid culture

  • Retrieved supernatant
  • Added 20 g/L HP-20
  • Stirred at RT for 2 h
  • Filtration with Buchner funnel to retain HP-20
  • Washed with 400 ml dddH2O
  • Elution with 400 ml Methanol
  • Evaporated methanol with rotary evaporator
  • Resuspended in 2 ml 50 methanol : 50 ddH2O

Protocol for pellet

  • Kept pellet
  • Washed pellet with destilled water
  • Resuspended pellet in 50 ml destilled water
  • Freeze and thawed 8 times
  • Centrifugation at 3750 rpm for 30 min
  • Kept supernatant
  • Added 20 g/L HP-20
  • Stirred at RT for 2 h
  • Filtration with Buchner funnel to retain HP-20
  • Washed with 400 ml dddH2O
  • Elution with 400 ml Methanol
  • Evaporated methanol with rotary evaporator
  • Resuspended in 2 ml 50 methanol : 50 ddH2O

MICRO-TOF

File:Heidelberg 20131004 MicroTOF.pdf

Result

Unexpectedly, the D. acidovorans positive control was negative for expression of Delftibactin. The results are therefore inconclusive and the experiment has to be repeated.

Thanks to

Retrieved from "http://2013.igem.org/Team:Heidelberg/Delftibactin/Delftibactin"