Team:BIOTEC Dresden/Modeling v2
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=== Theory behind FLP-FRT recombination === | === Theory behind FLP-FRT recombination === | ||
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- | 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 Flp reporter system as a powerful PoPS measurement device. | + | 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. |
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- | + | === 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). | ||
- | + | [[Image:Kinetic_FLP_1.png]] | |
- | |||
- | + | '''Figure 1'''Steps 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).<br> | ||
+ | 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.<br> | ||
+ | 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:<br> | ||
- | + | 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).<br> | ||
- | + | 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. |
Revision as of 10:31, 21 October 2009
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
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 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).