Team:BIOTEC Dresden/Modeling v2

Theory behind FLP-FRT recombination

In genetics, FLP-FRT recombination is a site-directed recombination technology used to manipulate an organism's DNA under controlled conditions in vivo. It is analogous to Cre-Lox recombination. It involves the recombination of sequences between short Flippase Recognition Target (FRT) sites by the Flippase recombination enzyme (FLP or Flp) derived from the 2µ plasmid of the baker's yeast Saccharomyces cerevisiae.

The 34bp long FRT site sequence is : 5'-GAAGTTCCTATTCtctagaaaGTATAGGAACTTC-3'. Flippase (flp) binds to the 13-bp 5'-GAAGTTCCTATTC-3' and to the reverse complement of 5'-GTATAGGAACTTC-3' (5'-GAAGTTCCTATAC-3'). The FRT site is cleaved just before 5'-tctagaaa-3', the 8bp asymmetric core region, on the top strand and behind this sequence on the bottom strand.[1]

Several variant FRT sites exist. Recombination can occur between two identical FRT sites but generally not between non-identical FRT sites.

Many available constructs include the sequence 5'-GAAGTTCCTATTCC-3' immediately upstream the FRT site (resulting in 5'-GAAGTTCCTATTCCGAAGTTCCTATTCtctagaaaGTATAGGAACTTC-3') but this sequence is dispensable for recombination.

Because the recombination activity can be targeted to only one target organ, or a low level of recombination activity can be used to consistently alter the DNA of only a subset of cells, FLP-FRT can be used to construct genetic mosaics in multicellular organisms. Using this technology, the loss or alteration of a gene can be studied in one target organ of interest, even if experimental animals could not survive the loss of the gene in other organs.

The effect of altering a gene can also be studied over time, by using an inducible promoter to trigger the recombination activity late in development - this prevents the alteration from affecting overall development of an organ, and allows single cells lacking the gene to be compared to normal neighboring cells in the same environment.

A very similar study using eukaryotic DNA: http://www.ncbi.nlm.nih.gov/pubmed/10581237

kinetic analysis of Flp activity - DNA binding and recombination models: http://www.ncbi.nlm.nih.gov/pubmed/9813124

Thermostability of Flp recombinase (We are using the F70L variant because it is sufficiently slow to give a time course): http://www.ncbi.nlm.nih.gov/pubmed/8932381

http://www.recombineering.net/img/A202_01.gif

pCAGGS-FLPe-IRESpuro expression vector.

Unlike transcriptional regulation, this method gives true all-or-none induction due to covalent modification of DNA by Flp recombinase. Determining the transfer curve of inter-FRT site distance versus average recombination time allows the onset of gene expression to be predicted. We then apply this [http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2009&group=BIOTEC_Dresden Flp reporter system] as a powerful PoPS measurement device.

Recombination pathway of FLP: design of mathematical model

The recombination pathway upon which the mathematical model for recombination was based is shown in Figure 1. The model describes an excision reaction on a linear DNA substrate. The steps of DNA binding are well characterised for FLP. The enzyme binds the inverted repeat target site first as a monomer, which is then joined by a second monomer to form a dimer Andrews et al., 1987; Hoess et al., 1984; Mack et al., 1992). In the model, we have assumed that the protein is monomeric in solution, based on the behaviour of FLP and Cre in sucrose density gradients under similar buffer conditions to those used in this study (Abremski & Hoess, 1984; Qian et al., 1990).

Figure 1Steps in FLP and Cre excision recombination reaction. Inverted repeat target sites are shown as open arrows. Recombinase monomers are shown as filled circles. Each step in the reaction is reversible and has a forward and a backward rate, indicated by small arrows. The forward and backward rate constants for each step are indicated on the Figure beside the arrows (small kn or k-n). The equilibrium constant for the conversion of one complex to another is given by the quotient of the backward and forward rate constants. Equilibrium constants are indicated (Kn). Names of species used for mathematical modelling are shown beside each complex (Ringrose et al., 1998, reproduced with permission).

In our scheme, the second-order association rate constants for the binding of the first and second monomers are named k1 and k2, respectively. This process must occur twice to occupy both target sites of the excision substrate. In the model, all DNA binding and dissociation steps are described by k1 and k2, and their corresponding first-order dissociation rate constants, k-1 and k-2 (Figure 1). A reduced model, describing the sequential binding of recombinase monomers to a single full site target comprising two half sites, in terms of the four parameters k1, k2, k-1 and k-2 is described by equations (7) to (10) (see below).
After DNA binding, the next step in the pathway is synapsis. FLP synapsis occurs by random collision (Beatty et al., 1986). In Figure 1, synapsis of the fully occupied excision substrate is described by a single first-order rate constant, k3. The model only allows for intramolecular synapsis, although in reality intermolecular recombination can also occur. However, for recombination assays, standard experimental conditions have been used, under which the frequency of intermolecular recombination is negligible. The multiple steps of catalysis are well characterised for FLP (for reviews, see Stark et al., 1992; Jayaram, 1994; Sadowski, 1995), and are described in Figure 1 by a single pair of rate constants, k4 and k-4, the forward and back rates of catalysis, respectively.
At present, we do not have a means of accurately measuring the formation of the synaptic complex. For this reason, we have further simplified the model by combining the constants k3 and k4 to give an apparent constant, k34, describing the rate of conversion of the fully bound substrate (SM4) into the excised synaptic complex (IEP) (Figure 1). The back rate, k-34, describes the reverse process. The relationship between k34, k-34 and their components k3, k-3, k4 and k-4 is given by:

k34/k-34 = (…k3 x k4)/(k-3 x k-4)

In this scheme, the dissociation of the synapse is represented as a reversal of its assembly: dissociation gives rise first to two products, each of which is bound by a recombinase dimer (Figure 1). This process is described by the first-order rate constant, k5. The dissociation of recombinase from DNA is assumed to occur in a stepwise manner, and is described in the model by the rate constants k-1 and k-2 (Figure 1). This assumption is based on the most simple and logical pathway. The dissociation mechanism of FLP has not been studied extensively, and there is disagreement in the literature regarding the steps involved. In experiments with synthetic Holliday junctions, it has been reported that the resolution of such structures requires two (Dixon & Sadowski, 1993), three (Qian & Cox, 1995) or four molecules of FLP (Lee et al., 1996). Based on experiments using full recombination substrates, Waite & Cox (1995) proposed a mechanism for FLP dissociation in which one or more monomers leave the synapse after recombination whilst others remain bound for longer. In the absence of a consensus on the mechanism of dissociation, Ringrose et al. (1998) proposed the mechanism shown in Figure 1, and point out that other mechanisms could easily be incorporated into the model by modification of equations (11) to (24) (see below).

The DNA binding rate constants k1, k-1, k2, k-2, and their corresponding equilibrium constants K1 and K2, have been directly measured using the gel mobility shift assay. If the DNA binding constants are known, this leaves two pairs of unknown rate constants: k34 and k-34, and k5 and k-5 (Figure 1). The mathematical model describes a general excision recombination reaction in which four protein monomers are required to reversibly recombine a single substrate, giving two products. The values of all rate constants, and of protein and substrate input can be varied to represent specific cases.