Team:HKUST-Hong Kong/characterization.html

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Characterization Data

1. BBa_K524000 –oriR101 & repA101-ts: This heat sensitive origin of replication origin has been shown to be function at 30°C Partial loss of plasmid happens at 33°C, and complete loss of plasmid is observed at 37°C.


2. BBa_K524001 –pLac + RBS + sfGFP1-10: This contains coding DNA sequences for superfolder GFP amino residues 1-214 driven by RBS BBa_B0034 and pLac BBa_R0010.


3. BBa_K524002 –pLac + RBS + sfGFP11 + double terminator: This contains coding DNA sequences for superfolder GFP amino residues 215-238 driven by RBS BBa_B0034 and pLac BBa_R0010, with double terminator B0015 at the end.


4. BBa_K524003 – nadE gene + double terminator: an essential gene that encodes constitutive expressed NAD+ synthatase.


5. BBa_K524004 –pir gene: the pir gene encodes the autogenously regulated pi protein.


6. BBa_K524005 – pToolkit: A plasmid that is only maintained in strains with genotype pir+. The plasmid was modified from another plasmid pKD46, which has been shown to trigger DNA recombination and subsequent gene knockout under induction of arabinose.


7. BBa_K524006 –RBS + sfGFP1-10: This contains coding DNA sequences for superfolder GFP amino residues 1-214 driven by RBS BBa_B0034.


8. BBa_K524007 –RBS + sfGFP11 + double terminator: This contains coding DNA sequences for superfolder GFP amino residues 215-238 driven by RBS BBa_B0034, with double terminator B0015 at the end.


9. BBa_K524100 – bcr CDS + double terminator B0015: The gene product is responsible for multidrug efflux system that pumps out antibiotics. Effect of pump was documented by other researchers: it confers varying degrees of resistance to 5 antibiotics.

Characterization Data for BBa_K524000

Heat sensitive origin of replication (oriR101 & repA101-ts)

Abstract

oriR101 & repA101-ts constitute a low copy origin of replication derived from the pSC101 replication origin. Initiation of replication at oriR101 is regulated in trans by the heat-labile protein product of repA101-ts, which is significantly denatured at 37°C. Hence when bacteria harbouring plasmids with this origin are incubated at 37°C, the activity of this origin would decrease, while temperatures higher than 42°C would cause the construct to cease its functions completely. (Datsenko, K.A. and Wanner, B.L. 2000).

In the process of its fabrication, a point mutation was introduced so as to make the construct compatible with Biobrick standard assembly requirements. Nevertheless, our characterization results do not seem to suggest great impacts to the construct's functions, causing only a slight increase in its thermosensitivity.

Construction of this part

This construct was cloned out from the pKD46 plasmid harboured in the E. coli strain BW25113 (courtesy of The Coli Genetic Stock Center). A single nucleotide mutation, performed through overlapping PCR, was introduced to eliminate a SpeI cut site originally present inside the construct between the promoter and CDS of the repA-ts gene. The mutation has been successfully confirmed by restriction digestion (Figure 1) and nucleotide sequencing.

#Figure 1: Digestion with SpeI for confirmation of mutation success

Characterization

• Construct preparation for heat sensitivity test

Characterization of the oriR101&repA101-ts was done with the insert ligated to RFP reporter and harbored in partregistry’s standard assembly pSB1AK3 plasmid. The enzymes Pst1 and Sma1 were then used to cut out the normal replication origin (pMB1) of pSB1AK3 and part of its KanR gene. The linearized plasmid was then allowed to self- ligate and transformed to DH10b E. coli strain. Restriction digestion test, along with the presence of red fluorescence and absence of Kanamycin resistance, is used as an indicator for plasmid verification. The final construct used for thermosensitivity test is referred to as “ori-ts” for convenience.

• Characterization method

Qualitative test

For construct thermosensitivity test, serial dilution was performed to well- grown overnight culture of ori- ts- positive cells. Dilutions done were aimed to give the following bacterial concentrations: ~1 cell/7μl, ~10 cells/7μl, ~100 cells/7μl, and ~1000 cells/7μl. A droplet 7μl in volume from each dilution dose in the series was applied on Amp plate and incubated at a specific incubation temperature. Four parallel sets of experiment was done, each incubated at 30°C/ 33°C/ 37°C/ 42°C. To give us an idea about the accuracy of dilutions performed, the above protocol was repeated with LB- only plates instead of LB+Amp plates

Quantitative test

To quantitatively determine the elimination rate of plasmids bearing our oriR101&repA101-ts, theoretically equal numbers of ori-ts- harboring bacterial cells were spread on an of LB+ Amp plate (labeled as Amp_ori-ts) and LB- only plate (labeled as LB_ori-ts). Four copies of this experimental setup were made for overnight incubations at four different temperatures: 30°C/ 33°C/ 37°C/ 42°C. Then, single colonies formed on the plates after overnight incubation were quantified. For each set, ratio of colony count on Amp_ori-ts plate to that on LB_ori-ts was calculated. The same protocol described above was applied to the same E.coli strain (DH10b) containing only the plasmids pKD46 and pBlueScript to serve as controls.
The total elimination rate of plasmid with thermosensitive replication origins (both mutated version in pSB1AK3 and unmutated version in pKD46) is computed by the following formula:

• Characterization result

• Qualitative test

Several sets of serial dilution tests are done at 30°C, 33°C, 37°C and 42°C. The image proof and the result summary are shown below.

#Figure 2: Qualitative Description of the temperature sensitivity test data.

For each temperature group, from left to right: 10-fold serially diluted O/N cultures beginning with the least diluted one. Refer to Characterization Method, Qualitative Test

A robust growth of ori-ts- positive cells was observed when the cells were incubated at 30°C. This robustness-indicated by the density of bacterial colonies in each droplet-covered region, and associated with proper functioning of plasmid's heat sensitive origin-steadily declined as the incubation temperature was increased. Partial replication origin dysfunction was observed after 33°C incubation and near- complete loss of function was observed at 37°C. Comparing this trend with the testing result of the unmutated oriR101&repA101-ts in pKD46 (partial loss of function observed at 37°C, and near- complete function at 42°C), the mutated one shows higher thermosensitivity.

• Quantitative test

The primary result of the quantitative thermosensitive test and trend of the elimination rate of ori-ts is shown by the following graph.

#Figure 3: Quantitative Analysis of the temperature sensitivity origin.

Conclusion

This pKD46- derived oriR101&repA101-ts displays obvious thermosensitive properties, which have seemed to intensified due to the point mutation introduced during the fabrication of the construct. The optimal incubation temperature for plasmid maintenance purpose is 30°C, whereas the recommended temperature for plasmid loss induction is 37°C or above.

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