# Patent

## Title
Method for the selection of recombinant clones comprising a sequence encoding an antidote protein to toxic molecule

## Abstract

The present invention is related to a method for the selection of recombinant clones having integrated a gene of interest and a nucleotide sequence encoding a functional antidote protein to a toxic molecule, wherein said recombinant clones are the ones which survive following their integration into a host cell comprising in its genome a nucleotide sequence encoding said toxic molecule. The present invention is also related to a nucleic acid construct, a vector comprising said nucleic acid construct, a host cell and a cloning and/or sequencing kit for performing said method.

## Background
INCORPORATION BY REFERENCE TO ANY PRIORITY APPLICATIONS
This application is a continuation of U.S. patent application Ser. No. 10/468,536 (now U.S. Pat. No. 8,470,580) filed on Jan. 23, 2004, which is the U.S. National Phase of International Application PCT/BE02/00021 filed on Feb. 22, 2002 designating the U.S. which was published in English as WO 02/066657 on Aug. 29, 2002, and which claims priority to U.S. Provisional Application No. 60/271,204 filed on Feb. 23, 2001. U.S. patent application Ser. No. 10/468,536 is incorporated by reference in its entirety.


FIELD OF THE INVENTION
The present invention is in the field of the recombinant DNA technology.
More precisely, the present invention is related to a method, to a nucleic acid construct, to a vector and to a cell used for the selection of recombinant clones comprising a sequence encoding an antidote protein to a toxic molecule.
BACKGROUND OF THE INVENTION 
1. State of the Art
It is possible to clone DNA inserts into vectors without ever select for recombinants and instead spend time in identification by hybridisation with radio-labelled probes, screen by restriction of small-scale preparations of plasmids or screening based on the inactivation of the alpha complementation in presence of X-Gal (blue/white screening).
These approaches used for more than one decade are not adapted to large scale cloning projects coming downstream complete genomes sequencing programs. The sequence information available has increased tremendously and will increase further in the future.
In order to assess the biological function of a coding sequence which has been identified, its corresponding gene in the genome of an organism must be specifically mutated (deleted or modified) (for instance in a knock-out mouse), which allows the study of phenotype(s) related to the mutation introduced. The specificity of the 5 mutation is given by a targeting vector (constructed in E. coli) containing homologous recombination arms.
If the development of sequencing technologies has permitted to increase tremendously the number of sequenced genes, cloning and sub-cloning genes at large scale in order to have recombinant clones and get information about the function of the corresponding genes is still a limiting step to functional genomic programs.
Cloning and sub-cloning each gene represent the bottleneck of the “functional genomic” programs. Therefore, new cloning approaches allowing speeding up these processes are required.
Because the identification of recombinants is a limiting step, it is clear that the positive selection of recombinants is required to move from traditional approaches to high throughput cloning allowing working with thousands of genes.
Cloning vectors permitting direct selection (positive selection) of recombinant strains have been proposed (for example, see Pierce et al. 1992; Kuhn et al. 1986). However, most cloning vectors present the following drawbacks: (i) they cannot be used to incorporate large nucleotide fragments, (ii) they are not easy to manipulate and (iv) they cannot be produced by a micro-organism in a large number of copies without bringing about the death of said micro-organism.
Furthermore, traditional restriction and ligase reactions can be replaced by site-specific recombination and recombinants be selected by the replacement of the ccdB gene (a member of the poison/antidote gene family) by the insert of interest (U.S. Pat. Nos. 5,910,438, 6,180,407 and International Patent WO 99/58652).
The main advantages of the ccdB-containing vectors over the other positive selection systems are i) the small size of their selective gene (ccdB: 303 bp), ii) the fact that the vector can be amplified in a host harbouring a mutation that confers total resistance to the CcdB poison (gyrA462 resistant strain; Bernard and Couturier, 1992). Since E. coli is the host used for most molecular cloning strategies, it is important to develop new systems which can enrich and widen the range of cloning possibilities. The positive selection technology using ccdB has been used to derive new vectors adapted to peculiar purposes: PCR cloning vectors (Gabant et al. 1997), vectors adapted for bacterial genetics (Gabant et al. 1998), and recently a kid gene belonging to the CcdB family has been used to design new cloning vectors (Gabant et al. 2000 and WO 01/46444).
Another example of the use of the CcdB gene is given by U.S. Pat. No. 5,888,732. This document discloses the general principle of the cloning method known as “the Gateway system.” In this method, the traditional restriction and ligase reactions are replaced by site-specific recombination sites and the recombinants are selected by inactivation (by deletion) of the ccdB gene by the gene of interest. This method allows rapid and efficient transfer of all the genes from an organism from one vector to different vectors (i.e. expression vectors) by automatic sub-cloning. The resulting sub-clones maintain the orientation as well as the reading frame allowing translation fusions (for a general overview, see Hartley et al. 2000).
However, said techniques are based upon counterselectable genes requiring, the use of rpsl, tetR, sacB or ccdB counterselectable genes, which can generate a seamless second round product that carries no “scar” from the first round of recombination.
Counterselection (selection for the inactivation or deletion of a toxic gene) is typically less efficient than positive selection (acquisition of a new property) as the intended recombination is only one of the several solutions for counterselection pressure. Any mutational event that ablates expression of the counterselectable genes, will also grow under counterselection pressure.
Thus for rare genetic events (which frequency can be compared to the mutational inactivation of the counterselectable gene), candidates from second-round counter-selection strategies, need to be screened to find the intended recombination event.
In practice, it seems that the ratio of the intended to unwanted products varies widely (from <1% to 15%-85%) for reasons that are still undefined (Muyrers G. P. P., Trends in Biochemical Sciences, Vol. 26, no. 5, p. 325-331, 2001).
AIMS OF THE INVENTION
The present invention aims to provide a new and improved method and products which do not presents the drawbacks of the state of the art and which allow an improved positive selection of recombinant clones.
A specific aim of the present invention is to provide such method and products which allow the selection of rare genetic events, especially the selection of recombinant clones having integrated long DNA fragments.
Another aim of the present invention is to propose a method and products which are not affected or less affected by the development of resistance mutations in the cells used for said positive selection.
SUMMARY OF THE INVENTION
A first aspect of the present invention is related to a method for the selection of recombinant clones having integrated a gene of interest and a nucleotide sequence, encoding a functional antidote protein to a toxic molecule (to a cell, preferably a prokaryote cell), wherein said recombinant clones are the ones which survive following their integration into a host cell comprising in its genome a nucleotide sequence encoding said toxic molecule.
Another aspect of the present invention is related to products used to perform said method, especially to a nucleic acid construct comprising at least one cassette nucleotide sequence made of at least one nucleotide sequence encoding an antidote protein to a toxic molecule (to a cell, preferably to a prokaryote cell) and a gene of interest or an insertion site for said gene of interest (preferably, said insertion site being not present in the nucleotide sequence encoding the antidote protein); said cassette nucleotide sequence being disposed between a first recombination site and a second recombination site in said nucleic acid, construct (said first recombination site and said second recombination site do not recombine with each other).
According to a preferred embodiment of the present invention, the antidote protein and the toxic molecule are respectively, an anti-poison protein and a poison protein. Said anti-poison or poison proteins could be wild type proteins or modified proteins which are naturally or artificially poisonous and affect one or more vital functions of a cell (preferably, a prokaryote cell) and may lead to the killing of the cell.
The antidote protein and the toxic molecule are preferably selected from the group consisting of CcdA/CcdB proteins, K is/Kid proteins, Phd/Doc proteins, SoK/HoK proteins, RelB/relE proteins, PasB (or PasC)/PasA proteins, mazF/mazE proteins or any other couple of anti-poison/poison molecules which are or are not of plasmid origin.
The toxic molecule can also be a toxin protein being naturally or artificially toxic and affecting one or more vital functions of a (prokaryote) cell.
The protein encoded by the gene sacB (from Bacillus amylolique-faciens), the protein GpE, the protein GATA-1 and the protein Crp are other examples of such toxic molecules.
The gene sacB encodes the levan sucrase which catalyses the hydrolysis of sucrose into products which are toxic for E. Coli (Pierce et al., Proc. Natl. Acad. Sci., Vol. 89, No. 6 (1992) p. 2056-2060). The protein GpE encodes the E genes from the bacteriophage φX174 which includes six unique restriction sites and encodes gpE and which causes lysis of E. Coli cell (Heinrich et al., Gene, Vol. 42, No. 03 (1986) p. 345-349). The protein GATA-1 has been described by Trudel et al. (Biotechniques, 1996, Vol. 20(4), p. 684-693). The protein Crp has been described by Schlieper et al. (Anal. Biochem., 1998, Vol. 257(2), p. 203-209).
The antidote proteins to said toxic molecule are any protein able to reduce or suppress the effect of the corresponding toxic molecule on a cell (preferably a prokaryotic cell), when said toxic molecule is produced by said cell.
According to another embodiment of the present invention, the nucleotide sequence encoding the antidote protein is a first nucleotide fragment encoding an inactive antidote protein, which can be rendered active 5 (functional) following correct integration of the gene of interest in the cassette sequence.
Preferably, the cassette sequence present in the nucleic acid construct according to the invention comprises also promoter/operator sequences in order to obtain the expression of the antidote protein which can be expressed constitutively or following the insertion of the gene of interest (insert) or by a recombination event.
For instance, the antidote activity can be achieved when the gene of interest (insert) brings a sequence comprising a transcriptional and/or translation signal that allows the expression of the antidote protein or when the gene of interest integrates another antidote sequence, a portion of it or its C-transcriptional or translation signal through insertion or by a recombination event.
By said mechanism, the correct insertion of the gene of interest inside the nucleic acid construct can also be advantageously selected.
Said gene of interest may also further comprise a promoter/activator sequence which allows or improves the expression of said antidote protein or comprises a second nucleotide fragment which will complement the first nucleotide fragment of said antidote protein in order to render said antidote protein functional (active against the toxic molecule).
According to a further embodiment of the present invention, the insertion site of the gene of interest is a cloning site, such as a recombination site or a nucleotide sequence specifically cleaved by one or more restriction enzymes.
Advantageously, the insertion site for said gene of interest is comprised in a nucleotide sequence encoding a toxic molecule, preferably a poison protein. Therefore, the nucleic acid construct according to the invention is based upon firstly, a negative selection which following the integration of the gene of interest into the nucleotide sequence encoding the toxic molecule inactivates said sequence and secondly a positive selection which allows thereafter, the expression of an antidote protein.
This double selection allows, advantageously, an improved selection of recombinant clones with rare genetic events, such as the integration of a very long DNA fragments, inside the nucleic acid construct according to the invention.
In the nucleic acid construct according to the invention, the first and the second recombination sites, recognised by recombinase(s), are preferably att phage λ based sites (specific recombination sites such as the ones described by Ptashne M. et al. (Genetic switch, Cell Press, Cambridge, 1992). Preferably, said att sites are integrated into a nucleic acid construct according to the invention by the method described by Landy A. et al. (Annual Review, Biochemistry, Vol. 58, p. 913, 1989).
However, other types of recombination sites can be also integrated into the nucleic acid construct according to the invention.
Another aspect of the present invention is related to a vector (an autonomously replicating vector such as a plasmid, a bacteriophage, a virus, a cationic vesicle or any other type of vector) comprising the nucleic acid construct according to the invention.
A preferred embodiment of the present invention is related to a vector donor, DNA molecule comprising a first DNA segment and a second DNA segment, said first or second DNA segment containing as selectable marker at least one nucleotide sequence encoding an antidote protein to a toxic molecule, and wherein said first and second DNA segment is flanked by at least a first and second recombination site, which do not recombine with each other.
Said selectable marker in the vector DNA molecule according to the invention may also comprise at least one inactive fragment of the antidote sequence and a functional selectable marker is obtained, when recombining across said first and second recombination sites with a further DNA segment comprising the inactive fragment of said selectable marker (other fragment of the antidote sequence).
In the vector donor DNA molecule, the recombination sites are the above-described recombination sites, preferably selected from the group consisting of the various recombination sites such as the ones described in U.S. Pat. No. 5,888,732.
The vector donor DNA molecule according to the invention is advantageously combined in a kit of parts (preferably, in a cloning kit) with an insert donor DNA molecule, said insert donor DNA molecule comprising the first DNA sequence flanked by the first recombination site and a second recombination site which do not recombine with each other. The characteristics of said insert DNA molecules are the ones described in U.S. Pat. No. 5,888,732 and patents WO99/21977, WO01/31039, WO01/42509 incorporated herein by reference.
Another aspect of the present invention is related to a cell, possibly integrated in the above-mentioned kit, preferably a prokaryotic host cell for the vector or the nucleic acid construct according to the invention, said cell having incorporated in its chromosomal DNA, at least one (preferably, at least two or more) nucleotide sequence(s) encoding the toxic molecule (for which the nucleotide sequence present in the nucleic acid construct is encoding an antidote), the expression of said toxic molecule being negatively repressed (controlled), preferably by a transcriptional and/or translation repressive tool, for instance, by adding to said nucleotide sequence encoding the toxic molecule a repressive promoter/operator nucleotide sequence which allows a transcriptional and/or translation repressive control of said protein poison and avoid the death of the cell.
However, said repressive control can be removed by adding or suppressing the addition of a specific compound to the cell (i.e.: a saccharide), which allows the expression of the toxic molecule by the cell.
Furthermore, the activity of the toxic molecule could be also conditional (for example, by introducing in the cell a thermosensitive allelle or a specific amber mutation suppression).
Furthermore, the cell could comprise also an antidote which is expressed in specific conditions and is able to block the deleterious effect of said toxic molecule in the cell.
Preferably, the cell according to the invention is an E. Coli cell which has the deposit number LMGP-21399.
Said cell was deposited in the Laboratorium voor Microbiologie—Universiteit Généralement, K. L. ledeganckstraat 35, B-9000 Gent, Collection of the Belgian Coordinated Collection of micro-organisms, BCCM, under no. LMGP-21399, on the date of Feb. 15, 2002. Said deposit has been made in accordance with the provision of the Budapest treaty regarding the international recommission of the deposit of micro-organisms.
Another aspect of the present invention is related to the use of said products for the selection of recombinants and to a method for selecting recombinant clones comprising the step of providing a cassette sequence in the nucleic acid construct or the vector according to the invention or inserting a gene of interest in the insertion site provided in said cassette sequence, transform the cell according to the invention with the nucleic acid construct or the vector according to the invention and selecting recombinant cell clones which survive.
The present invention will be described in more details in the following non-limiting example.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 depicts a nucleic acid construct 1 according to the invention.
FIG. 2 is schematic representation of the CYS10 construct.



DETAILED DESCRIPTION OF THE INVENTION
Description of Plasmids and Strains
The FIG. 1 describes a nucleic acid construct 1 according to the invention which comprises a cassette nucleotide sequence 2 made of a nucleotide sequence 3, encoding an antidote protein 4 to a toxic molecule 5 and a gene of interest 6 or an insertion site for a gene of interest 6, and a promoter/operator sequence 9; said cassette sequence 2 being disposed between a first recombination site 7 and a second recombination site 8, said first and second recombination site(s) 7, 8 do not recombine with each other.
Said nucleic acid construct 1 is advantageously integrated into a vector which is an insert donor DNA vector 10 comprising a further selectable marker 11. Said insert DNA donor vector 10 can be combined with an insert acceptor DNA vector 12, comprising a recombination site 13 and another selectable marker 14, said insert donor DNA vector 10 and said insert acceptor vector or molecule 12 after recombination form the recombinant vector 15 according to the invention. The correct recombination orientation will be selected by using the characteristics of the selective marker 11 and by using a bacterial strain expressing in its chromosome one or more genetic sequence(s) encoding the toxic molecule 5.
In the present case, the nucleotide sequence encoding an antidote protein 4 is a nucleotide sequence encoding the CcdA protein, which is the antidote to the toxic molecule 5 (CcdB protein), expressed by the bacteria.
The first selectable marker 11 presented in the insert donor DNA vector 10 is the protein poison kid and the second selectable marker 14 is a genetic resistance to an antibiotic (ampicyline).
Advantageously, the insert donor DNA vector 10 could be amplified in a bacteria which is resistant to the activity of the first selectable marker 11, for instance, a bacteria expressing the antidote protein kis to the protein poison kid.
Such bacteria comprising constitutively the kis sequence is described in the document WO01/46444 and protected by the deposit number LMGP-19171.
Another aspect of the present invention concerns the strain host cell 20 wherein the selection of the recombinant clones is performed.
The preferred strain is an Escherichia coli strain CYS10, which is a derivative of DH10B strain (mcrA Δ(mrr-hsdRMS-mcrBC)φ80lacZdM15 ΔlacW74 endA1 recA1 deoRΔ(ara, leu}7697 araD139 ga/U ga/K nupG rpsL, commercialized by Invitrogen). This strain carries a ccdB poison gene 21 under the control of the Ptac promoter 22 in the dcm gene of the chromosome, a defective λ expressing the Red and Gam functions under the control of λ PERFLUOROCARBON LIQUID promoter and the temperature sensitive CI857 repressor (description of this system: Yu et al., 2000, PNAS 97:5978-5983) and two plasmids (Pulb3566 23 n Psc101Laclq 24). The pULB3566 plasmid 23 produces the CcdA antidote 3 under the control of the Pbad promoter and carries the ampicilline resistance gene. The Psc101 laclq 24 plasmid produces the Laclq repressor and carries the spectinomycine resistance gene. The Ptac promoter 22, controlling the expression of the ccdB poison gene, is repressed by the Laclq protein, and is induced by the addition of IPTG 26 (isopropyl β-D thiogalactoside, C9H18O5S, Roche; 0.5 mmole/litre) in the culture media. However, even in the presence of the Laclq protein, the Ptac promoter 22 is not completely repressed causing a residual expression. The Pbad promoter, controlling the expression of the ccdA antidote gene 3, is completely repressed in the absence of arabinose 25 and induced by the addition of arabinose 25 (1%) in the culture media (Guzman et al., 1995, Journal of Bacteriology, Vol. 177, p. 4121-4130).
Due to the temperature sensitive DI857 repressor, the strain grows only at 30° C. Due to the presence of ccdB in the chromosome, the strain grows only in the presence of arabinose allowing the production of the CcdA antidote. Consequently, the strain grows at 30° C., in LB medium and in presence of arabinose (1%).














CcdA
CcdB
CYS10 strain


Media
production
production
at 30° C.







LB + Ara (1%)
Yes, Induced
Yes, residual
Growth


LB
No, repressed
yes, residual
No growth


LB + IPTG (0.5 mM)
No, repressed
Yes, induced
No growth


LBa = Ara(1%) +
Yes, induced
Yes, induced
Growth


IPTG(0.5 mM)









The schematic representation of the CYS10 construction is presented in FIG. 2.
However, the characteristics of said bacterial strain can be improved by the deletion of thermosensitive characteristic and by the introduction of additional genetic sequences encoding more toxic molecules in order to reduce or avoid the selection of mutants which are resistant to the activity of said toxic molecule (ccdB production).

## Claims

1. A method for the selection of recombinant clones, said method comprising:
obtaining a prokaryotic host cell comprising in its genome a nucleotide sequence encoding a poison protein; and
introducing an insert comprising a first nucleotide sequence encoding a first portion of a functional antidote protein to the poison protein and a second nucleotide sequence of interest, into a third nucleotide sequence encoding a second portion of the functional antidote protein to generate a nucleotide sequence encoding a functional antidote protein to the poison protein, wherein said recombinant clones are the ones which survive following introduction of said nucleotide sequence encoding a functional antidote protein to the poison protein into the host cell;
wherein the antidote and poison proteins are selected from the group consisting of the following coupled proteins: CcdA/CcdB protein, Kis/Kid protein, Phd/Doc protein, RelB/relE protein, PasB/PasA protein, PasC/PasA protein and mazE/mazF protein.

2. The method of claim 1, further comprising recovering one or more recombinant clones.

3. The method of claim 1, wherein the insert further comprises a promoter/operator sequence from which the nucleotide sequence encoding a functional antidote protein to the poison protein is expressed.

4. The method of claim 1, wherein the insert further comprises a transcriptional and/or translational signal of the nucleotide sequence encoding the antidote protein to the poison protein.

5. The method of claim 1, wherein said insert brings a sequence comprising a transcriptional and/or translational signal that allows the expression of the functional antidote protein or a C-terminal, transcriptional or translational signal of the functional antidote protein.

6. A method for the selection of recombinant clones, said method comprising:
obtaining a prokaryotic host cell comprising in its genome a nucleotide sequence encoding a poison protein; and
introducing an insert comprising a first nucleotide sequence encoding at least a portion of a functional antidote protein to the poison protein and a nucleotide sequence of interest, wherein said insert does not produce a functional antidote protein to the poison protein, into a second nucleotide sequence to generate a nucleotide sequence which produces a functional antidote protein to the poison protein, wherein when the first nucleic acid sequence encodes a portion of a functional antidote protein to the poison protein said second nucleotide sequence encodes a second portion of the functional antidote protein, and wherein said recombinant clones are the ones which survive following introduction of said nucleotide sequence which produces the functional antidote protein to the poison protein into the host cell,
wherein the antidote and poison proteins are selected from the group consisting of the following coupled proteins: CcdA/CcdB protein, Kis/Kid protein, Phd/Doc protein, RelB/relE protein, PasB/PasA protein, PasC/PasA protein and mazE/mazF protein.