Difference between revisions of "Part:BBa K3034000"

(→‎Characterization of CrpP function)
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<partinfo>BBa_K3034000 short</partinfo>
 
<partinfo>BBa_K3034000 short</partinfo>
  
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CrpP is a novel ciprofloxacin(CIP)-modifying enzyme which can phosphorylate CIP. Then the phosphorylated CIP goes through multiple steps of degradation spontaneously and produces 1,4-dihydroquinoline finally[1]. 1,4-dihydroquinoline is used as a kind of new carriers for specific brain delivery [2], so we can infer that it's nontoxic. This part is responsible for degradation of ciprofloxacin in our project.
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CrpP is a novel ciprofloxacin(CIP)-modifying enzyme which can phosphorylate CIP. Then the phosphorylated CIP goes through multiple steps of degradation spontaneously and produces 1,4-dihydroquinoline finally[1]. 1,4-dihydroquinoline is used as a kind of new carriers for specific brain delivery [2], so we can infer that it has certain value. This part is responsible for degradation of ciprofloxacin in our project.
  
 
<!-- Add more about the biology of this part here
 
<!-- Add more about the biology of this part here
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===Molecular weight===
 
===Molecular weight===
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This gene codes for a protein of 65 amino acids with a molecular mass about 11 kDa.When with a 6×Histag, the weight reaches about 15kDa.
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This gene codes for a protein of 65 amino acids with a molecular mass about 11 kDa.When followed by a 6×Histag, the weight reaches about 15kDa.
  
 
===Expression of CrpP-His===
 
===Expression of CrpP-His===
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In order to detect CrpP’s function, High Performance Liquid Chromatography (HPLC) was chosen. Although HPLC has a relatively higher sensitivity, the concentration of CIP inferred from the Km and Vmax given by Víctor M. Chávez-Jacobo et al.(2018) [1] is beyond HPLC’s limit of detection(LOD). So, we had to low down the CIP’s concentration. However, it was difficult to tell the difference between experimental group(CrpP+) and control group(CrpP-) directly through peak shape in such a low CIP concentration(＜1mg/L).  
 
In order to detect CrpP’s function, High Performance Liquid Chromatography (HPLC) was chosen. Although HPLC has a relatively higher sensitivity, the concentration of CIP inferred from the Km and Vmax given by Víctor M. Chávez-Jacobo et al.(2018) [1] is beyond HPLC’s limit of detection(LOD). So, we had to low down the CIP’s concentration. However, it was difficult to tell the difference between experimental group(CrpP+) and control group(CrpP-) directly through peak shape in such a low CIP concentration(＜1mg/L).  
  
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Statistics methods were introduced to help to solve this problem. Same concentration of CIP was incubated in a 1.9mL mix including 2 mM ATP, with or without cell extract that contains CrpP, at 37℃ for 30 minutes. Our experimental group(CrpP+) has 30 samples and control group(CrpP-) has 6 samples. Reaction was terminated by adding 2μL Concentrated Hydrochloric Acid. It is reasonable to reckon that the average peak area of both group has no difference in the beginning, but we can clearly notice that the experimental group’s average peak area is lower than that of control group(Fig. 2). Moreover, T-test for comparison of pooled data mean was introduced to analyze our results. T-test results indicate that in the case of a probability of error of less than 5%, there is a significant difference between the experimental group(CrpP+) and the control group(CrpP-). Thus, we can come to the conclusion that CrpP has the capability of degrading CIP.
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Statistics methods were introduced to help to solve this problem. Same concentration of CIP was incubated in a 1.9mL mix including 2 mM ATP, with or without cell extract that contains CrpP, at 37℃ for 30 minutes. Our experimental group(CrpP+) has 30 samples and control group(CrpP-) has 6 samples. Reaction was terminated by adding 2μL Concentrated Hydrochloric Acid. It is reasonable to reckon that the average concentration of CIP of both group has no difference in the beginning, but we can clearly notice that the experimental group’s average concentration is lower than that of control group(Fig. 2). Moreover, T-test for comparison of pooled data mean was introduced to analyze our results. T-test results indicate that in the case of a probability of error of less than 5%, there is a significant difference between the experimental group(CrpP+) and the control group(CrpP-). Thus, we can come to the conclusion that CrpP has the capability of degrading CIP.
 
[[File: Degradation of CIP by CrpP.png|500px|thumb|center|'''Fig. 2. ''' Degradation of CIP by CrpP  
 
[[File: Degradation of CIP by CrpP.png|500px|thumb|center|'''Fig. 2. ''' Degradation of CIP by CrpP  
 
(CrpP-: E.coli without crpP gene;CrpP+: E.coli express CrpP)]]
 
(CrpP-: E.coli without crpP gene;CrpP+: E.coli express CrpP)]]

Revision as of 17:02, 18 October 2019

CrpP：Ciprofloxacin-Modifying Enzyme

CrpP is a novel ciprofloxacin(CIP)-modifying enzyme which can phosphorylate CIP. Then the phosphorylated CIP goes through multiple steps of degradation spontaneously and produces 1,4-dihydroquinoline finally[1]. 1,4-dihydroquinoline is used as a kind of new carriers for specific brain delivery [2], so we can infer that it has certain value. This part is responsible for degradation of ciprofloxacin in our project.

Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]

Characterization

Molecular weight

This gene codes for a protein of 65 amino acids with a molecular mass about 11 kDa.When followed by a 6×Histag, the weight reaches about 15kDa.

Expression of CrpP-His

Because expression of CrpP-Histag is unsatisfying in E.coli DH5α, so we clone pelB-5D, CrpP with 6×Histag and TagRFP CDS into an expression vector, then the vector is transformed into E.coli BL21(DE3). 0.5mM IPTG is used for protein's expression and (over)expression is monitered by 17% SDS-PAGE.

Fig. 1. SDS-PAGE analysis of TagRFP and CrpP-His from E.coli DH5α co-transformed piGEM2019-01 and piGEM2019-02(a) and E.coli BL21(DE3) transformed pEASY with pelB-5D, CrpP, Histag and TagRFP(b). In (a), lane 3,4 were the IPTG induction group, lane 1,2 were the control group. In (b), lane 1,2 were the IPTG induction group, lane 3,4 were the control group.

Characterization of CrpP function

In order to detect CrpP’s function, High Performance Liquid Chromatography (HPLC) was chosen. Although HPLC has a relatively higher sensitivity, the concentration of CIP inferred from the Km and Vmax given by Víctor M. Chávez-Jacobo et al.(2018) [1] is beyond HPLC’s limit of detection(LOD). So, we had to low down the CIP’s concentration. However, it was difficult to tell the difference between experimental group(CrpP+) and control group(CrpP-) directly through peak shape in such a low CIP concentration(＜1mg/L).

Statistics methods were introduced to help to solve this problem. Same concentration of CIP was incubated in a 1.9mL mix including 2 mM ATP, with or without cell extract that contains CrpP, at 37℃ for 30 minutes. Our experimental group(CrpP+) has 30 samples and control group(CrpP-) has 6 samples. Reaction was terminated by adding 2μL Concentrated Hydrochloric Acid. It is reasonable to reckon that the average concentration of CIP of both group has no difference in the beginning, but we can clearly notice that the experimental group’s average concentration is lower than that of control group(Fig. 2). Moreover, T-test for comparison of pooled data mean was introduced to analyze our results. T-test results indicate that in the case of a probability of error of less than 5%, there is a significant difference between the experimental group(CrpP+) and the control group(CrpP-). Thus, we can come to the conclusion that CrpP has the capability of degrading CIP.

Fig. 2. Degradation of CIP by CrpP (CrpP-: E.coli without crpP gene;CrpP+: E.coli express CrpP)

References

[1]Chávez-Jacobo, Víctor M., et al. CrpP is a novel ciprofloxacin-modifying enzyme encoded by the Pseudomonas aeruginosa pUM505 plasmid. Antimicrobial agents and chemotherapy 62.6 (2018): e02629-17.

[2]Foucout, Lénaïg, et al. Synthesis, radiosynthesis and biological evaluation of 1, 4-dihydroquinoline derivatives as new carriers for specific brain delivery. Organic & biomolecular chemistry 7.18 (2009): 3666-3673.