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Part:BBa_K2560036

Designed by: Tobias Hensel   Group: iGEM18_Marburg   (2018-09-15)


Phytobrick version of ColE1

This is the Phytobrick version of the Origin ColE1 and was build as a part of the Marburg Collection. Instructions of how to use the Marburg Collection are provided at the bottom of the page.

Overview

Origins of replication (Oris) are genetic elements where DNA replication is initiated. In plasmids the Ori sequence is responsible for it’s maintenance and for the copy number inside the cell (Selzer et al., 1983; Brantl, 2014).

The origins of replication colE1, pMB1 and p15A belong to the same family. They do not code for any enzyme but are replicated by the hosts RNA polymerase (Cesareni et al., 1991; Brantl, 2014). The polymerase transcribes a region 508 bp upstream the Ori sequence (Tomizawa & Itoh, 1981; Selzer et al., 1983) synthesizing a pre-primer RNA called RNA II. During transcription the RNA II underlies conformation changes building secondary structures(Brantl, 2014). This structures contain typical loops (Cesareni et al., 1991) that binds to the plasmids’ Ori sequence building an RNA-DNA hybrid (Cesareni et al., 1991; Brantl, 2014). The RNA II is than cleaved by the hosts RNase H to become a mature primer (Cesareni et al., 1991; Brantl, 2014).

Characterization

For our collection we characterized three Oris commonly used in molecular biology: colE1, pMB1 and p15A. We measured two different plasmids, one with and another without a LUX cassette. Both plasmids consist of a kanamycin resistance cassette and one of the three Oris described. The LUX expression plasmid contained a constitutively expressed LUX cassette of ~6kb. The other one contained a connector sequence to build an ‘empty’ plasmid. By comparing this constructs you may consider that the copy number is not only influenced by the LUX expression but also by the plasmids sizes. This Oris belong to the same family differing in mutations in the RNA I region (Tomizawa & Itoh, 1981; Selzer et al., 1983).

Figure 1: Empty construct for measuring the plasmids’ copy number.
It's an emty plasmide and was assembled from three basic parts (Origin, Connector and Kanamycin Resistance) by Golden Gate Assembly.
Figure 2: Lux construct for measuring the plasmids’ copy number.
The construct expressing Lux to get an influence on the copy number. The plasmide was assembled from four basic parts (Origin, Connector, Lux and Kanamycin Resistance) by Golden Gate Assembly.

We measured the plasmids’ copy number by qPCR using the absolute quantification method.
A qPCR is set up the same way like a normal PCR but with addition of a DNA binding fluorophore in this case SYBR Green. SYBR Green binds double stranded DNA emitting a high signal while unbound SYBR Green shows only low fluorescence (Zipper et al., 2004). In every PCR cycle the number of double stranded DNA is duplicated emitting an increasing fluorescence signal. This signal is detected after every cycle by the qPCR machine and the value is saved. After the run finished, normally after ~40 cycles, a signal threshold is determined and the corresponding cycle when the threshold was reached is saved for further analysis.
For the qPCR run first total DNA from our host containing the plasmids of interest was isolated in the exponential phase (OD600 ~ 0.5), purified using the innuPREP Bacteria DNA Kit from Analytik Jena and all samples normalized to ~5ng/ul with the Qubit fluorometer from ThermoFisher scientific. Subsequently a dilution series was made in 1.5ml tubes diluting the DNA 7 times 1:2. This way the dilution series contained 8 steps reaching from 20 to 2-7. Two different primer pairs were used for the analysis: one matching the housekeeping gene dxs present once on the genome and the other matching the kanamycin resistance cassette on the plasmid. The DNA samples used for the amplification of the kanamycin cassette were the same used for the dilutions 2-4 and 2-5. The threshold cycles (Ct) acquired in triplicates from the dxs sequence were used for a standard curve. By comparing the Ct values from the resistance cassette with the corresponding standard curve the number of copies could be determined as multiples from the dxs sequence. It should be considered that the dxs sequence is coded on the first chromosome of V. natriegens at ~ one o’clock. Due to that probably the sequence is present more than once because of multifork replication of the genome.

To build the standard curve the Ct values were plotted on the y-axis and the corresponding dilution steps on the x-axis. The x-axis was set logarithmic and the standard curve was calculated with Excel. The curve’s formula was than used to calculate the corresponding x-value from the resistance cassette’s Ct values. Because the x-values describe a theoretical dilution the Ct values were multiplied with this value and with their corresponding dilution to obtain the final amount of multiplies compared to the genome. For every Ori an own standard curve was calculated.

Result

In our experiments we showed that the plasmids’ copy number controlled by three different Oris differ a lot when comparing V. natriegens with E. coli.
One possible explanation might be different expression levels of RNA I and RNA II respecting the rate of RNA I – RNA II bounds (Cesareni et al., 1991) due to the divergent metabolism in V. natriegens and E. coli. Another plausible explanation might be the different methylation patterns in both organisms probable affecting the formation of the RNA II secondary structures and subsequently its binding affinity to the DNA (Russell & Zinder, 1987; Cesareni et al., 1991).

It was shown that mutations especially in the loop I structure might be responsible for Ori compatibility and copy number control (Selzer et al., 1983; Cesareni et al., 1991). The copy number is mainly determined by two factors: the binding efficiency of the RNA II to the DNA – specially controlled by the stabilization of stem-loop IV – (Cesareni et al., 1991) and the interference of the complementary RNA I to the RNA II pre-primer (Brantl, 2014). The RNA I is transcribed constitutively from the complementary strand from RNA II pre-primer (Brantl, 2014). Binding of RNA I to RNA II prevents the correct folding of the pre-primer (Brantl, 2014). This way the RNA-DNA hybrid can not be formed and subsequently the primer maturation can not take place (Brantl, 2014).


Figure 3: Quantification of plasmid copy number in dependency of different Oris.

The columns show the average of the calculated multiplies for the different plasmids. The blue columns show the numbers for the plasmids containing a ~6kb LUX cassette. The orange columns show the numbers for the ‘empty’ plasmids without reporter. For every column six measurements have been calculated. Looking at the ‘empty’ plasmids it is clearly shown that colE1 and p15A remain high copy plasmids like in E. coli with a copy number of ~200 copies per cell. For pMB1 the copy number is scaled down becoming a low copy number Ori in V. natriegens. Looking at the LUX plasmids it is clearly shown that the colE1 Ori remains at a high copy number while pMB1 and p15A drop down to a significantly lower level.


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]


Marburg Toolbox

We proudly present the Marburg Collection, a novel golden-gate-based toolbox containing various parts that are compatible with the PhytoBrick system and MoClo. Compared to other bacterial toolboxes, the Marburg Collection shines with superior flexibility. We overcame the rigid paradigm of plasmid construction - thinking in fixed backbone and insert categories - by achieving complete de novo assembly of plasmids.

36 connectors facilitate flexible cloning of multigene constructs and even allow for the inversion of individual transcription units. Additionally, our connectors function as insulators to avoid undesired crosstalk.

The Marburg Collection contains 123 parts in total, including:
inducible promoters, reporters, fluorescence and epitope tags, oris, resistance cassettes and genome engineering tools. To increase the value of the Marburg Collection, we additionally provide detailed experimental characterization for V. natriegens and a supportive software. We aspire availability of our toolbox for future iGEM teams to empower accelerated progression in their ambitious projects.


Figure 4: Hierarchical cloning is facilitated by subsequent Golden Gate reactions.
Basic building blocks like promoters or terminators are stored in level 0 plasmids. Parts from each category of our collection can be chosen to built level 1 plasmids harboring a single transcription unit. Up to five transcription units can be assembled into a level 2 plasmid.
Figure 5: Additional bases and fusion sites ensure correct spacing and allow tags.
Between some parts, additional base pairs were integrated to ensure correct spacing and to maintain the triplet code. We expanded our toolbox by providing N- and C- terminal tags by creating novel fusions and splitting the CDS and terminator part, respectively.


Parts of the Marburg Toolbox




Tags and Entry Vectors




  • K2560001 (Entry Vector with RFP dropout)
  • K2560002 (Entry Vector with GFP dropout)
  • K2560005 (Resistance Entry Vector with RFP Dropout)
  • K2560006 (Resistance Entry Vector with GFP Dropout)
  • K2560305 (gRNA Entry Vector with GFP Dropout)