# Patent

## Title
Method of effecting a change in a cell, and a vector

## Abstract

A method of effecting a change in a cell using a transfer system which is contacted with the cell to be changed. The transfer system comprises a fusion protein which is transferred into the cell using the VirB/VirD4 transfer system. According to the invention, a fusion protein BA is introduced into the cell to be changed comprising i) as a first part A, an oligopeptide comprising the C-terminal amino acids 1-20 of VirF, VirD2, VirE2, VirE3, VirD5 or MobA, or an analogue thereof and ii) as a second part B, a polypeptide capable of effecting a cell-changing activity in the cell to be changed, wherein the polypeptide is attached with the C-terminal end thereof linked with the N-terminal end of the first part.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is a continuation-in-part application of PCT International Application No. PCT/NL01/00388, filed on May 21, 2001 and designating the United States of America, published in English on Nov. 21, 2001 as WO 01/89283 A1, the contents of the entirety of which are incorporated herein by this reference.


TECHNICAL FIELD
The invention relates generally to biotechnology and, more specifically, to a method of effecting a change in a cell, wherein a transfer system is contacted with the cell to be changed, the transfer system comprising a membrane including a protein transport system comprising a pore which comprises a VirB complex and VirD4 protein, wherein the transfer system comprises a fusion protein or is capable of making a fusion protein which is introduced into the cell by means of the protein transport system.
BACKGROUND
Zhou, X-R et al. (Journal of Bacteriology, 181 (14), p. 4342-4352 (1999)) discloses that the protein VirE2, a single-stranded DNA-binding protein of Agrobacterium tumefaciens, can be transferred into a host cell by a tumorigenic Agrobacterium. Zhou et al. disclosed that they were only at amino acid 39 (from the N-terminus, as is customary in the art) able to introduce a heterologous amino acid sequence which was transferred to the host cell. Zhou et al. concluded that it was not practically feasible to base a protein delivery system on fusions at one of the two ends of VirE2. Small proteins at least are tolerated as an insertion at amino acid 39.
DISCLOSURE OF THE INVENTION
The invention provides a method of effecting a change in a cell, wherein a transfer system is contacted with the cell to be changed, the transfer system comprising a membrane including a protein transport system comprising a pore which comprises a VirB complex and VirD4 protein, wherein the transfer system comprises a fusion protein or is capable of making a fusion protein which is introduced into the cell by means of the protein transport system, which method is simple to perform and, if desired, is performed without native activity of VirE2 in the cell to be changed.
Accordingly, a method according to the invention is characterized in that a fusion protein BA is introduced into the cell to be changed in which fusion protein BA:
i) comprises, as a first part A, an oligopeptide comprising the C-terminal amino acids 1-20 of VirF, VirD2, VirE2, VirE3, VirD5 or MobA, or an analogue thereof and
ii) comprises, as a second part B, a polypeptide capable of exercising a cell-changing activity in the cell to be changed, wherein the C-terminal end of the polypeptide is linked to the N-terminal end of the first part A, under the condition that if the fusion protein comprises a first part A derived from VirE2, the fusion protein does not comprise the 84 N-terminal amino acids of VirE2.
Surprisingly, it has been found that, provided the above-mentioned conditions are met, a protein can be introduced from the outside into a cell to be changed, which protein is formed by coupling the polypeptide (second part B) to an (internal) N-terminal amino acid of VirF, VirD2, VirE2, VirE3, VirD5 or MobA or an analogue thereof (first part A), as a result of which the activity of the introduced second part B may be expressed in the cell to be changed, as a result of which the cell is changed. This change may be temporary (reversible) or permanent (irreversible). The amino acid sequences of VirF, VirD2, VirE2, VirE3, VirD5 and MobA are represented by the respective sequence nos. 1-6. A strain comprising a plasmid (LBA8250, a Agrobacterium tumefaciens strain, containing plasmid pTi15955. pTi15955 is described by Sciaky et al., Plasmid 1, p. 238-253 (1978)) coding for all vir proteins, is in the Phabagen collection of the Centraalbureau voor Schimmelcultures (CBS), Baarn, the Netherlands, under accession number PC2692. MobA protein is known from incQ plasmid RSF1010, as present in E. coli strain K12 C600 with accession number PC-V3110 of the NCCB collection of the CBS, and described by Scholz, P. et al. in Gene 75, p. 271-288 (1989).
As is shown in the Examples, the C-terminal parts of the peptides as mentioned can be shortened from the N-terminal end without significant loss of functionality of transport. Evidence is provided that the minimum number of amino acids of the C-terminal part of VirF required for the functionality of transport is about 20 amino acids, where a number of about 40 amino acids seems to be optimal. Further, a sequence comparison (with hand alignment, see Table 2) of the C-terminal parts of the sequences 1-6 has determined that all the sequences show the presence of at least two arginine(R) residues in the last few amino acids, while some have even four or more R residues in the C-terminal 20-mer. Also it is apparent from the sequences as presented that this C-terminal 20-mer predominantly consists of hydrophilic and neutral amino acids. Generally, no more than 10% of the amino acids are hydrophobic, but preferentially no more than 20%, more preferentially no more than 30%, even more preferentially not more than 40% and most preferably not more than 50%. It is to be understood that analogues of the C-terminal peptides as disclosed in this invention can also be used. Analogues can be formed by replacing, adding or deleting one or more amino acids from the C-terminal peptides of the amino acid sequences of virF, virE2, virE3, virD2, virD5 and mobA, but they still should comply with the above requirements (the C-terminal 20-mers having at least two R (or K, see below) residues and predominantly consisting of hydrophilic and neutral amino acids). For replacing amino acids, preferably corresponding amino acids are taken, but it is also envisaged that the amount of arginines/lysines and/or the amount of hydrophilic amino acids is increased. For example, it is very well possible to replace one or more of the R residues with a lysine (K) residue, without severe loss of functionality of transport.
In the present invention, a corresponding amino acid is an amino acid according to the following table:















A, G;



S, T;



D, E;



N, Q;



R, K;



I, L, M, V; and



F, Y, W.










The first part A may, if desired, comprise more amino acids from amino acid 21 (as from the C-terminus) of VirF, VirE2, VirE3, VirD2, VirD5 or MobA with the proviso for VirE2 as previously mentioned. Most preferred is a C-terminal part consisting of 40 amino acids of the mentioned peptides.
In the present invention, a vector is understood to be any DNA or RNA sequence which, directly or indirectly, leads to the formation of the fusion protein in the transfer system. Such a vector may be derived from an Agrobacterium Ti or Ri plasmid, but can also be derived from plasmids generally used in the area of transformation such as broad host range plasmids (e.g., pBBR, pBR322, pUC14, pBLUEscript, pGREEN and the like). Useful plasmids can also be found in the experimental section.
The vector will include all elements necessary for the production of the fusion protein AB as defined above and/or the protein transport proteins VirB and VirD4, such as promoters, transcriptional and translational enhancers, and terminators.
The transfer system may be a cell, such as, very suitably, a bacterial cell, such as in particular Agrobacterium tumefaciens, but may also be an artificial system, such as a minicell or an artificial vesicle system. It is to be understood that the transfer system further comprises all necessary elements to enable functionality of the system. In the case of Agrobacterium, this means that all the (genetic) information for survival or fitness of the bacterium needs to be present.
The fusion protein to be transferred can either be formed in the transfer system itself, for example, by expressing a vector containing a functional gene system that may be expressed yielding the fusion protein, or the fusion protein itself may be introduced into the transport system. In artificial transport systems, generally the latter will be the case. An important advantage of such an artificial transport system is that it may be introduced into the environment, for example, for treating a crop, without risk of spreading genetic material.



BRIEF DESCRIPTION OF THE FIGURES
FIG. 1 Schematic drawing of the test system in plants.
FIG. 2 Schematic drawing of the test system in yeast.
FIG. 3 Analysis of transport of Cre::virF fusion proteins into Arabidopsis excision line 3043 in two independent experiments. Cre: LBA1100 containing pSDM3147, wt: LBA1100 constaining pSDM3155 (Cre::virFdel1-126 wt), D185A, R187A, E189A, M191A, S192A (only exp. 2), D194A (only exp. 2), R195A, P196A (only exp. 1), R197A (only exp. 1), S198A, T199A (only exp. 2), R200A (only exp. 2), G201A (only exp. 2), L202A (only exp. 2): Single point mutations in cre::virFdel1-126.
FIG. 4 Analysis of transport of Cre::virF fusion proteins into Arabidopsis excision line 3043. Cre: LBA1100 containing pSDM3147, wt: LBA1100 constaining pSDM3155 (Cre::virFdel1-126 wt), R187A, R187D, R195A, R195K, R195D, R197A, R197K, R197D, R200A, R200D, R195/197A: Single point mutations in cre::virFdel1-126.
FIG. 5 Analysis of protein transport from Agrobacterium into yeast strain LBY2. Strain LBA1100 containing no plasmid (none), pSDM3147 (cre), pSDM3148 (virE2::Cre), pSDM3129 (Cre::virE2), pSDM3153 (NLS::virF::cre), pSDM3154 (NLS::cre::virF) or pSDM3155 (NLS::cre::virF::del1-126=42N). Efficiency is calculated as the number of yeast colonies growing on medium containing FOA/output number of yeast cells.
FIG. 6 Analysis of VirE3 protein transport from Agrobacterium into yeast in two independent experiments. Strain LBA1100 containing pSDM3147 (cre), or a plasmid expressing an NLS::cre::virE3, or NLS::cre::virE3 (50 C terminal amino acids). Efficiency is calculated as the number of yeast colonies growing on medium containing FOA/output number of yeast cells.



DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS
Preferably, the fusion protein is introduced into the cell without the introduction of a DNA or RNA sequence. In case of the use of A. tumefaciens as the transfer system, this implies the absence of T-DNA. This means that it is possible to change a cell without introducing genetic material into the cell to be changed.
According to one embodiment, the fusion protein introduced has recombinase activity. In such a case, it is, in fact, possible to effect a change in the chromosomal DNA of the cell to be changed without introducing additional genetic material (a vector coding for the T-DNA or peptide B) into the cell. An important application is, for example, the removal of a marker gene, whose admittance in the environment is undesirable. In particular, this may include the removal of antibiotic-resistance genes present between DNA sequences in direct repeat to be recognized by the recombinase.
Conveniently, a bacterium of the class of Rhizobiaceae may be used as a transfer system, such bacteria amongst which Agrobacterium, Rhizobium and Phyllobacterium are very suitable for modification of plants, yeasts or fungi. Other bacteria belonging to this family, such as Brucella, are known for their interaction with human and animal cells and may be used for modification thereof. Especially Brucella or other bacteria which can interact with mammalian cells are of particular interest for changing these cells. In this way, it would be possible to administer (proteinaceous) drugs which would not survive conventional dosage regimens, e.g., due to the presence of proteases. Also, vaccines based on such a protein delivery are envisaged.
According to a preferred embodiment, use is made of Agrobacterium, which is known to be very suitable for the modification of both prokaryotes (bacteria), and eukaryotes (plants, yeasts, fungi, and animal cells).
According to a preferred embodiment, a cell chosen from the group consisting of i) a plant cell; ii) a yeast cell; and iii) a fungal cell, is used as the cell to be modified. Such a cell may be changed according to the present invention in vitro or in vivo. When cells are changed in vitro, it is further envisaged that these cells can be used for regeneration of the organism (such as regeneration of plants or fungi and yeasts), but also, in the case of animal cells, for re-introduction into the body. This latter embodiment would be useful for overcoming (epi)genetic defects in mammalians, for example, by inducing directed (epi)genetic changes in pancreatic cells that do not correctly express insulin in diabetics.
The invention also relates to a vector, the vector being characterized in that it codes for a protein transport system comprising a pore which contains a VirB complex and VirD4 protein, as well as for a fusion protein BA that comprises i) as a first part A an oligopeptide comprising the C-terminal amino acids 1-20 of VirF, VirD2, VirE2, VirE3, VirD5 or MobA, or a part or an analogue thereof, and ii) as a second part B a polypeptide capable of effecting a cell-changing activity in the cell to be changed, wherein the polypeptide with its C-terminal end is linked to the N-terminal end of the first part A, under the condition that if the fusion protein comprises a first part A derived from VirE2, the fusion protein does not comprise the 84 N-terminal amino acids of VirE2. As stated above, also vectors which only code for a protein transport system comprising a pore which contains a VirB complex and VirD4 protein are part of the embodiment of the invention in which the fusion protein is added to the cell containing the vector.
Such a vector may be introduced into a transfer system, such as a bacterium. A vector according to the invention will possess the minimal information that needs to be expressed for the transfer of the fusion protein, making it possible for the fusion protein to be transferred to the cell to be changed.
Finally, the invention relates to a vector set, which is characterized in that the vector set comprises one or more vectors coding for a protein transport system comprising a pore which contains a VirB complex and VirD4 protein as well as a further vector coding for a fusion peptide BA which comprises i) as a first part A an oligopeptide comprising the C-terminal amino acids 1-20 of VirF, VirD2, VirE2, VirE3, VirD5 or MobA, or a part or an analogue thereof, and ii) as a second part B a polypeptide capable of exercising a cell-modifying activity in the cell to be modified, wherein the polypeptide of the C-terminal end of the polypeptide is linked to the N-terminal end of the first part A, under the condition that if the fusion protein comprises a first part A derived from VirE2, the fusion protein does not comprise the 84 N-terminal amino acids of VirE2.
The advantage of such a vector set is that the vector or vectors coding for the protein transport system may be introduced into a transfer system separate from further vector coding for the fusion protein. This makes it possible to use a transfer system, in particular a bacterium, as a standard vehicle for modifying a cell, wherein the transport system is provided with a further vector which is expressed in the transport system for effectuating the modification.
The protein translocation system of the invention can be used, amongst others:
a) for induction of systemic resistance to pests and diseases in plants, for example, by spraying plants with bacteria that transfer an anti-pathogenic protein, such as a chitinase, glucanase or osmotin, or with bacteria that contain a protein which triggers a so-called hypersensitive response, such as an avr protein or a mutated ndr protein;
b) for transdermal, subcutaneous, oral, intranasal, gastrointestinal or pulmonary delivery of a proteinaceous drug. This is especially useful for proteinaceous drugs, which application is hampered by their sensitivity to degradation in the body, e.g., by protease activity on the skin or in the mucosa. Also, it is deemed to be particularly useful to improve existing or design novel drugs that will provide solutions for unmet medical needs such as colon and skin cancer (antineoplastics), diabetes, psoriasis, infections (anti-inflammatory drugs) and genetic defects;
c) for development of vaccines for both human and veterinary applications;
d) for development of in vivo or in vitro diagnostic products, for instance, by introducing an enzyme that is capable of detecting a specific metabolite in plant, fungal (including yeast) or animal cells by converting it into a (fluorescent) dye or by enhancing the expression of a gene in the acceptor cell, which gene product can easily be detected;
e) for drug development. For this it is envisaged that a (high throughput) screen can be developed in 96-well or 384-well plates for peptides or proteins that result in a desirable and scorable effect in plant, fungal (including yeast) and animal cells, using, for instance, a (reverse) two-hybrid approach in yeast (Vidal and Endoch, TIBTECH, 17, 374-381, 1999) to screen for peptides that disrupt or allow a protein-protein interaction and thereby prevent or allow expression of a reporter gene, which expression can be detected by survival of the cells (FAO selection) or by a fluorescent dye (GFP, alkaline phosphatase).
The invention will be illustrated with reference to the following Examples and to the drawing in which FIGS. 1 and 2 schematically show a test system to demonstrate Cre activity in planta (FIG. 1) and in yeast (FIG. 2), respectively.
EXAMPLES
Bacterial Strains
Agrobacterium strain LBA1010 (Koekman et al., Plasmid 7 (1982); 119-132; Centraal Bureau voor Schimmelcultures; Baarn, the Netherlands, accession number: PC2805) possesses the wild type Ti-plasmid pTiB6 in a C58 chromosomal background. LBA 1100 (Beijersbergen et al., Science 256 (1992), 1324-1327; easily obtained by culturing CBS 102794, Centraal Bureau voor Schimmelcultures; Baarn, the Netherlands, deposited on 17 May 2000 in the absence of gentamycin for curing of plasmid pSDM 3155 and screening for the absence of the small (ca. 5.5 kb) plasmid) is a non-oncogenic derivative of LBA1010. To this end, both the left and right T regions in pTiB6 as well as tra and occ genes are replaced by a spectinomycin-resistance marker, resulting in plasmid pAL1100, wherein the Vir region remained intact. For the present application, several vir mutants, derived from LBA1100, resp. LBA 1142-1150 (Beijersbergen et al., Science 256 (1992), 1324-1327) were used (Table 1). LBA2561 contains a precise deletion of the virF gene in pAL1100 (Schrammeijer et al., Mol. Plant. Micr. Int. 5 (1998), 429-433). Transformation and growth of bacterial strains were performed as described elsewhere (Vergunst et al., Nucl. Acids Res. 26 (1998) 2729-2734) or according to general techniques known to the person skilled in the art (Sambrook et al., Molecular cloning. A lab manual. (1989)).
Plasmid Constructions
The coding region of the cre gene was cloned translationally to the virE2 and virF gene of pTi15955, under control of the respective vir promoter regions. Both N-terminal and C-terminal fusions were made. The plasmid constructions are detailed below.
The cre Control Plasmid
The coding region of the cre recombinase gene, present in plasmid pUC19cre (Mozo & Hooykaas, Mol. Gen. Genet. 236 (1992), 1-7), was cloned as an SphI/EcoRI fragment into pUC21 (Vieira & Messing, Gene 100 (1991), 189-194), resulting in pSDM3120. In order to remove the ATG starting codon, a PCR amplification was performed at the 5′-end of the cre gene with the primers cre1 (5′-ggcagatctgTCCAATTTACTG) (SEQ ID NO:1) and cre2 (5′-GATAATCGCGAACATCTTCAGG) (SEQ ID NO:2) on pSDM3120. After digestion of the PCR fragment with BglII and NruI (underlined), this fragment was exchanged for the corresponding fragment in pSDM3120 (resulting in creΔATG or pSDM3121). An SalI fragment of pRAL3248 (Melchers et al., Plant Mol. Biol. 14 (1990), 249-259) into which virE1 and virE2 (the last 30 3′-terminal base pairs being absent) including the virE promoter region are located, was cloned into the XhoI restriction side of pSDM3121 (pSDM3122). After full digestion of pSDM3122 with BglII and partial digestion with BstYI, followed by isolation of the vector fragment carrying the virE promoter, the virE1 coding area, the ATG starting codon of virE2, as well as cre (ΔATG), the cre gene was translationally linked through self closure to the ATG starting codon of virE2 (pSDM3126). As a result, the expression of the cre gene is controlled by the virE promoter. Subsequently, this construct was transferred as an StuI/XbaI fragment to the SmaI/XbaI-digested plasmid pRL662, resulting in pSDM3147, i.e., the cre control plasmid used in these experiments. The non-mobilizable plasmid pRL662 with a broad host range is obtained by replacing the kanamycin resistance gene as well as the mob region of pBBR1MCS2 (Kovach et al., BioTechn. 16 (1994), 800-802) with a gentamycin resistance marker (J. Escudero, European patent application 00200726.8).
The cre::virE2 Fusion
In order to create translational fusions between cre and virE2, the STOP codon of the cre gene was removed; to this end, a mutation in the STOP codon (italics) was introduced using PCR amplification on pSDM3126 DNA using the primers cre 6 (5′-acgcgtcgactATCGCCATCTTCCAGCAGGCGC) (SEQ ID NO:3) and cre 7 (5′-cCATCGATTGATTTACGGCGCTAAGG) (SEQ ID NO:4). After digestion with ClaI and SalI (underlined), the corresponding ClaI-SalI fragment of pSDM3126 was replaced (resulting in creΔSTOP or pSDM3127). An XhoI/NotI fragment of pBluevirE2 (ΔATG) containing the virE2 coding area, without the ATG start codon, was subsequently ligated into the vector pSDM3127 digested with SalI and NotI (pSDM3128). pBluevirE2 (ΔATG) was the result of cloning the VirE1-virE2 region (XhoI-SmaI) of plasmid pRAL3248 (Melchers et al., Plant Mol. Biol. 14 (1990), 249-259) in pBLUEscript (XhoI/EcoRV) (Alting-Mees and Short, Nucleic Acids Res. 17 (1989): 9494), subsequent to which virE1 and the ATG start codon of virE2 were removed using an XhoI-StuI linker (5′-tcgaGATCTTTCTGGCAATGAGAAATCCAGG (SEQ ID NO:5) and 5′-CCTGGATTTCTCATTGCCAGAAAGATC (SEQ ID NO:6). The cre::virE2 fusion was subsequently transferred to pRL662 (SmaI/XbaI) as an StuI/XbaI fragment of pSDM3128, resulting in pSDM3129 (cre::virE2 fusion).
The virE2::cre Fusion
An SalI fragment of pRAL3248 comprising virE1 and virE2 (the last 30 3′-terminal bases being absent) was cloned into pIC19R (Marsh et al., Gene 32 (1984): 481-485) (pSDM3123). In the subsequent cloning steps, cre was fused to the 3′-end of virE2, wherein at the same time, the last 30 3′-terminal bases of virE2, absent in pSDM3123, were restored. To this end, a BglII/NruI fragment of pSDM3122, comprising the 200 5′-terminal bases of cre, without the ATG start codon, was cloned into pIC19R (pSDM 3151). An SalI/BglII linker, consisting of the last 30 3′-terminal bases of virE2, was synthesized in order to remove the STOP codon of virE2 (italics) (5′-TCGACCGCGTAGCCAAAGCGTCAACAGCTTTcga (SEQ ID NO:7) and 5′-gatctcgAAAGCTGTTGACGCTTTGGCTACGCGG (SEQ ID NO:8)) and to effect translational fusion with cre. This linker was cloned into pSDM 3151 (pSDM3152). However, after sequence analysis, the BglII site between the 3′-end of virE2ΔSTOP and the 5′-end of creΔATG was shown to be lost due to a single base substitution. This mutation is not present in the region coding for virE2 or cre, and has no effect on the reading frame of the fusion. The SalI fragment of pSDM3123 was introduced into the SalI site of pSDM3152 (pSDM3157), cloning the complete virE2 sequence in frame with the 5′-end of cre. An NruI fragment of about 600 base pairs from pSDM3157 (the 3′-end of virE2ΔSTOP and the 5′-end of creΔATG) was subsequently used to replace the NruI fragment in pSDM3148 (pSDM3148 is the result of cloning an StuI/XbaI fragment of pSDM3122 into pRL662 XbaI/SmaI, resulting in a translational fusion between the complete virE2 region and cre (pSDM3166, i.e., the virE2::cre fusion) under control of the virE promoter and joint expression of VirE1.
The virF::cre Fusion
A 600 base pair SacI/EcoRV fragment of pRAL7088 (Schrammeijer et al., MPMI 11 (1998) 429-433) containing the 5′ flanking side of virF and the ribosomal binding place was cloned into pBluescriptSK− (Alting-Mees and Short, Nucleic Acids Res. 17 (1989): 9494), resulting in pSDM3183. The nuclear localization signal (NLS) of simian virus 40 (SV40) was synthesized with an EcoRV blunt and a 3′ SalI sticky end (5′-ATCATGGATAAAGCGGAATTAATTCCCGAGCCTCCAAAAAAGAAGAGAAAGGTCG AATTGGGTACCGG (SEQ ID NO:9) and the complementary strand) and cloned into pSDM3183, resulting in pSDM3184. The virF gene without the ATG and STOP codon was cloned in two steps in frame after SV40 NLS. The ATG start codon was removed by cloning a BamHI/NsiI linker (5′-GATCCGAAATTCGAGTTTGCGTGATGCA) (SEQ ID NO:10) in the BamHI and NsiI sites of pRAL7088 (pSDM3192). Subsequently, a BamHI/SacI fragment of 1.5 kilobase pairs of pSDM3192 was cloned into pIC19H (pSDM3193). An SalI/XhoI fragment of 500 base pairs of pSDM3193 comprising virFΔ498-609ΔATG was cloned in frame with the SV40 NLS into the XhoI site of pSDM3184, resulting in pSDM3185. Subsequently, the STOP codon of virF was removed using two primers (5′-ATCCCTAACTTGGTCTTCAAC (SEQ ID NO:11) and 5′-cttagatcTAGACCGCGCGTTGATCGAGG) (SEQ ID NO:12) in a PCR reaction on pRAL7088. The PCR fragment was subcloned as a 175 bp fragment into vector pGEM T (Promega). A 16 base pair StuI/BglII linker (5′-cctcgagcccgggata (SEQ ID NO: 13) and 5′-gatctatcccgggctcgagg (SEQ ID NO:14)) was cloned into pSDM3121 digested with StuI/BglII to introduce an XhoI site (underlined) and to effect further in-frame cloning of cre with virF (pSDM3121-L). Subsequently, the 3′-end of virF was cloned in frame into the XhoI/BglII sites of pSDM3121-L as an XhoI/BglII fragment of about 110 base pairs from the pGEM-T vector to the 5′-end of cre (resulting in pSDM3186). A 1.2 kb XhoI/SalI fragment of pSDM3186 was ligated into the XhoI site of pSDM3185, resulting in pSDM3187. The virF::cre fusion was subsequently introduced into pUC28 (Benes et al., Gene 130 (1993); 151-152) as a SacI/PstI fragment and subsequently ligated from this plasmid as an EcoRI fragment into the EcoRI site of pRL662, resulting in pSDM3153, i.e., the NLS::virF::cre fusion plasmid.
The cre::virF Fusions
A 0.66 kb fragment of pSDM3184, having the 5′ flanking side of virF and the SV40 NLS sequence, was eventually cloned via an SacI/SalI cloning step into pIC19H, followed by an HindIII/SalI cloning into pIC19R, as an SalI/XhoI fragment into the XhoI site of pSDM3121. This resulted in an in-frame fusion of the SV40 NLS to the 5′-end of cre (pSDM3188). The STOP codon of cre in pSDM3188 was subsequently removed by replacing the ClaI/SalI fragment (with the 3′-end of cre including STOP) with the ClaI/SalI creΔSTOP fragment of pSDM3127 (pSDM3179). A 690 bp SalI/EagI fragment of pSDM3193 comprising virFΔATG was cloned into pSDM3179 digested with SalI/NotI, resulting in pSDM3189. An HindIII/XbaI fragment of pSDM3189 was cloned into the HindIII and XbaI sites of pRL662, resulting in pSDM3154 (the NLS::cre::virF fusion plasmid).
In addition, a number of deletions was made of virF and cloned translationally to the 3′-terminus of cre. Using the primers F126 (5′-acgcgtcgaCCTGTCGAGTCGGCTGAG (SEQ ID NO:15), position 127 in virF) and pflF2 (5′-GACCAGCACACTTAGATACC (SEQ ID NO:16)) in the DNA sequence adjacent to 3′ virF), a PCR reaction was performed on pRAL7088. The PCR fragment of 780 base pairs was cloned into vector pT7pBlue-T (Novagen) (pSDM3194). An SalI/EagI fragment (virFΔ1-126) of 555 base pairs of pSDM3194 was cloned into pSDM3179, resulting in pSDM3190. Cloning the NLS::cre::virFΔ1-126 fusion into vector pRL662 as an HindIII/XbaI fragment resulted in pSDM3155 (the NLS::cre::virFΔ1-126 fusion plasmid).
The 113 3′-terminal nucleotides of virF were cloned in frame with cre. To this end, pSDM3189 was transferred as an HindIII/XbaI fragment to pUC18 (Yanish-Perron et al., Gene 33 (1985), 103-119), resulting in pSDM 3172. Digestion of pSDM3172 with XhoI and SalI, removal of the 5′-sticky end using Mung bean nuclease followed by self-closure of the vector resulted in an in-frame fusion of the last 112 3′-terminal base pairs of virF with cre (pSDM3173). Transfer of the NLS::cre::virFΔ1-498 fusion to pRL662 as an XbaI/HindIII fragment resulted in plasmid pSDM3174 (the NLS::cre::virFΔ1-498 fusion plasmid).
The plasmids were transferred to the bacterial strains shown in Table 1. In addition, the plasmid pSDM3191, on which the genes virD3 and virD4 are located under the control of the virD promoter, was mobilized in LBA1147 and LBA1150. pSDM3191 is the result of cloning a 4.4 kilobase pair BamHI fragment of pMP3 (Vogel and Das, J. Bacteriology 174 (1992), 5161-5164) in the BamHI restriction site of pLM997 (Melchers, unpublished), which is the result of replacing the T-region of pBin 19 (Bevan et al., Nucleic Acids Res. 12(1984), 8711-8721) with a pIC19R/H polylinker sequence (Marsh et al., Gene 32 (1984), 481-485).







TABLE 1







Strains used











Strain
Plasmid
Resistance-markers







LBA1010
pTiB6
Rif



LBA1100
pTiB6ΔT1,Tr, Δtra, Δocc
Rif, Sp



LBA2561
pAL1100ΔvirF
Rif, Sp



LBA1142
pAL1100(virΔ::Tn3Hohol)
Rif, Sp, Cb



LBA1143
pAL1100(virB4::Tn3Hohol)
Rif, Sp, Cb



LBA1144
pAL1100(virB7::Tn3Hohol)
Rif, Sp, Cb



LBAl145
pAL1100(virG::Tn3Hohol)
Rif, Sp, Cb



LBA1146
pAL1100(virC2::Tn3Hohol)
Rif, Sp, Cb



LBA1147
pAL1100(virD2::Tn3Hohol)
Rif, Sp, Cb



LBA1148
pAL1100(virD4::Tn3Hohol)
Rif, Sp, Cb



LBA1149
pAL1100(virE2::Tn3Hohol)
Rif, Sp, Cb



LBA1150
pAL1100(virD1::Tn3Hohol)
Rif, Sp, Cb










The NLS::cre::virF-fusion gene was also coupled to the helper plasmid in LBA2561 by selecting for single crossovers between the homologous DNA regions flanking the virF gene and NLS::cre::virF (pSDM3189), resulting in LBA2561::NLS::cre::virF.
As a control for transformation of the plant, LBA1115 (=MOG101, (Hood et al., Transgenic Res. 2 (1993), 208-218) was used, which is comparable to LBA1100 but containing tra and occ genes. IncP-vector pSDM3088 (Vergunst & Hooykaas, Plant Mol. Biol. 38 (1998), 393-406), containing the cre gene under control of the mannopine synthase promoter between the left and right adjacent sequences of Agrobacterium (“T-DNA border repeats”), was transferred to LBA1115.
Plant Lines
Plasmid pSDM3043 (see FIG. 1 and Vergunst & Hooykaas, Plant Mol. Biol. 38 (1998), 393-406) was introduced into Arabidopsis thaliana C24 by means of the Agrobacterium-mediated transformation of root explants (Vergunst et al., in Methods in Mol. Biol. 82 pp 227-244 (1998)) and transformants were selected for resistance to phosphinothricin (30 mg/l). Plants having the excision locus 3043 are sensitive to kanamycin. A transformed plant, with 3:1 segregation for the transgene (1 locus), was selected based on the efficiency of the Cre-mediated excision of the bar gene (see FIG. 1), flanked by lox sites present in direct repeat (see arrows in the drawing). Cre-mediated excision could be accomplished by transforming root explants with the Cre-expression vector pSDM3088. Such an excision simultaneously resulted in repair of a kanamycin resistance-marker.
Plant Transformation
The protocol for transformation of Arabidopsis root explants mediated by Agrobacterium was described earlier (Vergunst et al., in Methods in Mol. Biol. 82 pp 227-244 (1998)). Roots of 10-day old seedlings being homozygous for the excision locus 3043 (T3 or T4) were used in transformation assays using the strains disclosed in Table 1 containing the constructs described above. After co-cultivation for 2 days, the explants were transferred to a medium for inducing the growth of calli and shoots, which medium contained 50 mg/l kanamycin and 100 mg/l Timentin. The number of kanamycin-resistant calli was determined 2 and 3 weeks after co-cultivation. PCR analysis was performed on a number of shoots regenerated from calli resistant to kanamycin.
Construction of a Saccharomyces cerevisiae Strain Containing a Floxed URA3 Gene
The URA3 gene was cloned as an HindIII fragment from pJJ244 (Jones and Prakash (1990) Yeast, 6, 363-366) into the filled-in EcoRI site of pIC-2lox (Meijer et al. (1998) Yeast, 14, 1407-15) resulting in pSDM3011. The resulting floxed URA3 gene was subcloned as an HindIII fragment into pUC4α10 (Steensma et al. (1990) Eur. J. Biochem., 191, 769-74), which contains part of the PDA1 locus (pSDM3012). Finally, the PDA1-lox-URA3-lox-PDA1 cassette was cloned into binary vector pBin19 (Bevan (1984) Nucl. Acids Res., 12, 8711-21) resulting in pSDM3013. A. tumefaciens strain LBA1126 (Bundock and Hooykaas (1996) Proc. Natl. Acad. Sci. USA, 93, 15272-5) was electroporated (den Dulk-Ras and Hooykaas (1995) Methods Mol. Biol., 55, 63-72) with pSDM3013 and used in a co-cultivation experiment with S. cerevisiae strain RSY12 (MATa leu2-3, 112 his3-11, 15 ura3Δ::HIS3) (Schiestl and Petes (1991) Proc. Natl. Acad. Sci. USA, 88, 7585-9). Transformants, prototrophic for uracil, were selected on MY medium (Zonneveld (1986) J. Microbiol. Methods, 4, 287) containing 200 μM cefotaxime (Duchefa, B. V.), leucine (30 mg/l) and histidine (20 mg/l) but lacking uracil. Transformants were further characterized with polymerase chain reaction (PCR) and Southern blot analysis. Strain LBY2, in which the loxURA3lox gene had integrated at the PDA1 locus on chromosome V by homologous recombination (gene replacement), was selected and used in all co-cultivation experiments.
Yeast Co-Cultivation Experiments
Agrobacterium strains expressing the cre or cre-fusion gene were grown overnight at 29° C. in 5 ml MM (Hooykaas et al. (1979) J. Gen. Microbiol., 110, 99-109) supplemented with spectinomycin (250 μg/ml) and, in case a pRL662-based plasmid was present, also with gentamycin (40 μg/ml). Cells were harvested and diluted at an A600 of 0.25 in 5 ml induction medium (IM: MM salts and 40 mM 2-(N-morpholino) ethanesulfonic acid (MES), pH 5.3, 10 mM glucose, 0.5% (w/v) glycerol and 200 μM AS). The cells were then grown for 5 hours at 28° C.
S. cerevisiae strain LBY2 was grown overnight at 30° C. in 10 ml YPD medium (Sherman (1991) Methods Enzymol., 194, 3-21). Cells were diluted 1:10 in fresh 100 ml YPD medium and grown for 5 hours at 30° C. The cells were subsequently washed with and resuspended in 500 μl IM. 100 μl of the Agrobacterium and Saccharomyces cultures were mixed 1:1, and the mixture was placed on 0.45 μm cellulose nitrate filters on IM medium containing 5 mM glucose and the amino acids leucine and uracil at a concentration of 30 mg/l. To prevent loss of pRL662, gentamycin was added to the medium. After 6 days of co-cultivation at 22° C., the mixture was resuspended in 2 ml NaCl solution (9g/l) and 100 μl aliquots were plated out on solid MY medium supplemented with leucine, uracil, 200 μM cefotaxime and 0.1% fluoro-orotic acid (FOA). Ura− colonies were selected after 4 days growth at 30° C. The output number of Agrobacterium cells was determined on solid LC medium supplemented with spectinomycin or gentamycin. The output number of Saccharomyces cells was determined on solid MY medium with cefotaxime and the amino acids leucine and uracil.
PCR Analysis
The method used for isolation of chromosomal DNA for PCR analysis and the protocol for the PCR reaction were described earlier (Vergunst et al., Plant Mol. Biol. 38 (1998), 393-406). As primers (a and b in FIG. 1) for the analysis of kanamycin-resistant calli and plants use was made of:
a) 5′-GAACTCGCCGTAAAGACTGGCG-3′ (SEQ ID NO:17) annealing in the 35S promoter region (pDE35S in FIG. 1); and
b) 5′-GCGCTGACAGCCGGAACACG-3′ (SEQ ID NO:18) annealing in the nptII coding sequence (see FIG. 1). Primers used for plasmid construction are mentioned in detail.
Results
To show that Agrobacterium transfers fusion proteins into recipient plant cells, a recombination assay was used that allows the detection of the transport of the Cre recombinase. To this end, in experiments using Arabidopsis as host cells, the plant cell nucleus contained a DNA segment which, after specific deletion by Cre, results in a selectable kanamycin-resistance trait. This substrate for Cre recombination (pSDM3043, FIG. 1) was transferred by Agrobacterium-mediated transformation into the genome of Arabidopsis by means of selection for resistance to phosphinothricin. The transgenic plants were sensitive to kanamycin. However, the Cre-mediated recombination between two in tandem oriented lox sites results in excision of the intervening DNA segment and in the activation of the nptII gene by translational fusion of the 35S promoter region including the ATG start codon and an N-terminal coding part (determined by the lox sequence) with the coding region of nptII. This fusion leads to kanamycin resistance. Thus, only cells in which a Cre-mediated recombination event has taken place survive on the selective medium. A plant line was isolated, comprising a single locus of the excision substrate and whose excision efficiency (as measured by the number of kanamycin-resistant calli due to Cre activity) was comparable to that of the efficiency of Agrobacterium-mediated transformation. This was tested by co-cultivation of the plant line with an Agrobacterium strain carrying a binary vector with a T-DNA harboring the cre gene driven by a strong promoter sequence (LBA1115-pSDM3088). The selected excision line was used in further assays to prove direct protein transport, including the Cre-recombinase, from Agrobacterium to plant cells. To this end, Cre-recombinase was expressed under control of the vir-induction system in Agrobacterium, either alone or as an N-terminal or C-terminal fusion with VirF or VirE2, respectively. Expression of the fusion proteins in Agrobacterium was tested by immunoblot analysis (data not shown). Recombination activity of the fusion proteins was assayed by measuring the ability to induce an excision event in plasmid pSDM3043, which plasmid was introduced into the relevant bacterial strains in order to test this effect (data not shown).
After co-cultivation of the above-mentioned plant cells with the Agrobacterium-strains LBA1010, LBA1100, LBA1149, or LBA2561, or with a derivative of these strains harboring a plasmid expressing Cre-recombinase (the cre control plasmid), at most one single survivor was found on a selective medium. Thus, the same number of kanamycin-resistant calli (“the background”) was obtained during co-cultivation with strains which do not express Cre as during co-cultivation with Agrobacterium strains which do express Cre-recombinase. Thus, we conclude that bacterially expressed Cre-recombinase is not transferred to plant cells.
The results were, however, totally different when experiments were done with Agrobacterium cells expressing fusion proteins between Cre and VirE2 or VirF. Agrobacterium strains were used (both wild type as well as mutants for the respective Vir protein) which express either C-terminal or N-terminal fusions of Cre with VirE2 and VirF, respectively. It was found that the fusion at the N-terminal region of the Vir protein (Cre::VirE2; NLS::Cre::VirF), but not at the C-terminal end (VirE2::Cre; NLS::VirF::Cre), was highly efficient in producing kanamycin-resistant calli. No difference was observed whether the Cre::VirF-fusion was expressed from the helper plasmid (LBA2561::NLS::cre::virF) or from plasmid pRL662 (LBA2561, pRL662 NLS::cre::virF). Co-cultivation of Agrobacterium strains (both wild type and virF mutant) expressing a Cre::VirF-fusion with a deletion of the 42 N-terminal amino acids of virF (NLS::Cre::VirFΔ1-126) resulted in kanamycin-resistant calli being obtained at a significantly higher frequency. Co-cultivation of a strain expressing a fusion protein between the last 37 C-terminal amino acids of VirF and Cre (NLS::Cre::VirFΔ1-498) resulted in comparable high numbers of kanamycin-resistant calli.
As controls, strains harboring the fusion plasmids NLS::cre::virFΔ1-126 and cre::virE2 were co-cultivated with wild type Arabidopsis C24 root explants, but as expected, these did not result in kanamycin-resistance due to the absence of the excision locus.
PCR-analysis proved that kanamycin resistance was indeed caused by the predicted Cre-mediated excision event. PCR analysis on DNA isolated from the excision line 3043 resulted in a fragment of 2.3 kb (see FIG. 1), whereas in DNA samples isolated from kanamycin-resistant calli which were obtained after co-cultivation of strains expressing cre::virE2 and NLS::cre::virF, a 0.7 kb fragment is obtained. To exclude contamination with a T-DNA vector expressing cre, a PCR analysis was performed with primers annealing in the cre coding region. As expected, no fragment was detected.
PCR analysis of the few calli obtained from the control experiments (including those from experiments in which cultivation took place with an Agrobacterium strain not harboring a cre gene) showed that these were partly the result of an excision, possibly due to homologous recombination between the lox sites and partly due to continuing growth of sensitive plants on the selection medium (“escapes”). In the latter case, the 2.3 kb fragment was detected, and not the 0.7 kb fragment indicating excision. All these results thus show that Agrobacterium can introduce Cre-recombinase into plant cells, but only when expressed as a fusion protein attached to the N-terminus of VirE2 or VirF. The efficiency of obtaining kanamycin-resistant calli after co-cultivation of plant line 3043 with the Agrobacterium strains expressing fusions of Cre with 161 or 37 C-terminal amino acids of VirF shows that there must be a transport domain in the last 37 C-terminal amino acids of VirF. In addition, a fusion protein between the C-terminal 20 amino acids of VirF Cre was still transported, but with lower efficiency.
In view of the in planta function of VirE2, virF and VirD2 shown before, the three invariant amino acids (RPR-motif) in the C-terminus of VirF, VirE2 and VirD2 suggest the importance of these amino acids for the transport of the Vir proteins to the plant, using the VirB/VirD4 system (see later). Mutation of one of the R residues in this motif leads to a decrease in transport efficiency, but when the P residue in a residue chosen from A, Q, V and S was changed, the transport activity remained intact. To gain further insight into the translocation signal, mutagenesis of the C-terminus of VirFΔ1-126 was performed, according to Sawano and Miyawaki (2000, NAR 28, e78). The 18 C-terminal amino acids were independently changed into alanine residues (D185A, R187A, E189A, M191A, S192A, D194A, R195A, P196A, R197A, S198A, T199A, R200A, G201A and L202A). The mutant fusion proteins were assayed for efficiency of transport in Arabidopsis excision line 3043. Data from 2 representative experiments are shown in FIG. 3. Clearly, most single amino acid mutations have no significant impact on the efficiency of detection of transport. However, mutation of either of the arginine residues R187, R195, R197 or R200 resulted in a reduced efficiency with which transport is detected. R187 and R200 show to be most important, but not essential because transport can still be detected. A closer look was taken at the R residues by changing these amino acids into the basic lysine (K), or acidic aspartate (D) (FIG. 4). R187D, R195K, R195D, R197K, R197D, R200D, and R195/197A have been tested, and in these experiments, it appeared that after changing the arginine residue into a lysine residue, still considerable activity was left (see, FIG. 4).
In the present experiments, transport of the fusion proteins, detected as kanamycin resistance after co-cultivation with plant line 3043, occurs independent of co-transfer of T-DNA. This implies an important application of the protein transport system, namely, the possibility of effecting a change in cells in the absence of T-DNA. In addition, however, transfer may also occur in the presence of T-DNA (that may or may not be oncogenic), which broadens the applicability of the system. Possible application may be site-directed integration of T-DNA in the genome of the recipient cell by means of cotransport of a recombinase that is expressed as a fusion protein in the same or in cotransforming bacteria.
To determine which of the virulence functions are essential for protein transport, NLS::cre::virFΔ1-126 and cre::virE2 were transferred into a set of vir mutants, listed in Table 1.
Co-cultivation of the excision line with the virA, virB, virG and virD4 mutants, which harbor the fusion plasmids, did not result in Cre-mediated excision, whereas virC, virD1/D2, virF and virE2 mutants resulted in calli with efficiencies comparable to the efficiencies of the wild type. Thus, we can conclude that, in this model system wherein VirA and VirG are responsible for forming VirB and VirD4, expression of vir genes through the regulators VirA and VirG is necessary for transport. The virB genes and virD4, determining the type IV secretion channel (B-complex) and the coupling factor (VirD4), are essential. The occurrence of virB and virD4 homologs in other systems (for example, O'Callaghan et al., Mol. Microbiol. 33 (1999), 1210-1220) makes it possible to construct similar protein transport systems in Agrobacterium and other microorganisms based on these homologous systems. The other virulence genes, including those coding for the transported proteins VirD2, VirE2 and VirF, appeared not to be necessary for transport of the fusion proteins.
To prove that under the same conditions Agrobacterium will transfer fusion proteins into other eukaryotic cells, a recombination assay similar to the one described above was performed with yeast cells (FIG. 2). The yeast cells do not grow in the presence of 5-fluoro uracil, unless a recombinase removes the gene present between lox sites, which gene encodes a protein that converts 5-fluoro uracil into a substance that is toxic for the yeast cell. The recombinase was introduced as a fusion protein. As expected, the thus-treated yeast became resistant to 5-fluoro uracil (see, FIG. 5). In these experiments, the transport of the recombinase by means of the C-terminus of VirE2 and VirF was confirmed and, in addition, the transport via the C-termini of VirE3 (see, FIG. 6) and the MobA protein of the incQ plasmid RSF1010 was shown (results not shown). In the VirE3 protein, the RPR sequence is also present in the C-terminus, in VirD5 an RDR sequence is present and in MobA the RQR sequence is present. In addition, transport of the 50 C-terminal amino acids of VirD5 was confirmed into plants. Alignment of the C-termini of VirE2, VirF, VirE3, VirD2, VirD5 and MobA (see Table 2) shows that the C-terminus is hydrophilic.









SEQ ID NO:1












Amino acid sequence of virF_15955(1-609)




Universal code



Total number of amino acids: 202, MW = 22394



Max ORF: 1-606, 202 AA, MW = 22394



ORIGIN











1
MRNSSLRDAS GSNDAQVPHK




 



21
TELLNLPDHV LTEVAKRLAT



 



41
NNPVESAENI ANFSKSHRFT



 



61
RDAVRTEPLE KFSSRLKILS



 



81
RNAKLLSHAV RHAATLPDGE



 



101
QLSEAQLSQM RSEVATRPVL



 



121
GVAYTHQDGQ PEERLSGNHL



 



141
DHKINNIPNL VFNVAEPIMF



 



161
NEISALEVMA EVRPIARSIK



 



181
TAHDDARAEL MSADRPRSTR



 



201
GL*



 









SEQ ID NO:2












Amino acid sequence of VirD2_pTi15955(1-1275)




Universal code



Total number of amino acids:424, MW = 47476



Max ORF: 1-1272, 424 AA, MW = 47476



ORIGIN











1
MPDRAQVIIR IVPGGGTKTL




 



21
QQIINQLEYL SRKGKLELQR



 



41
SARHLDIPVP PDQIRELAQS



 



61
WVTEAGIYDE SQSDDDRQQD



 



81
LTTHIIVSFP AGTDQTAAYE



 



101
ASREWAAEMF GSGYGGGRYN



 



121
YLTAYHVDRD HPHLHVVVNR



 



141
RELLGHGWLK ISRRHPQLNY



 



161
DGLRKKMAEI SLRHGIVLDA



 



181
TSRAERGIAE RPITYAEHRR



 



201
LERMQAQKIQ FEDTDFDETS



 



221
PEEDRRDLSQ SFDPFRSDPS



 



241
TGEPDRATRH DKQPLEQHAR



 



261
FQESAGSSIK ADARIRVSLE



 



281
SERSAQPSAS KIPVIGHFGI



 



301
ETSYVAEASV RKRSGIFGTS



 



321
RPVTDVAMHT VKRQQRSKRR



 



341
NDEEAGPSGA NRKGLKAAQV



 



361
DSEANVGEQD TRDDSNKAAD



 



381
PVSASIGTEQ PEASPKRPRD



 



401
RHDGELGGRK RARGNRRDDG



 



421
RGGT*



 









SEQ ID NO:3












Amino acid sequence of virE2_pTi15955(1-1602)




Universal code



Total number of amino acids: 533, MW = 60502



Max ORF: 1-1599, 533 AA, MW = 60502



ORIGIN











1
MDLSGNEKSR PWKKANVSSS




 



21
TISDIQMTNG ENLESGSPTR



 



41
TEVLSPRLDD GSVDSSSSLY



 



61
SGSEHGNQAE IQKELSALFS



 



81
NMSLPGNDRR PDEYILVRQT



 



101
GQDAFTGIAK GNLDHMPTKA



 



121
EFNACCRLYR DGAGNYYPPP



 



141
LAFDKISVPA QLEETWGMME



 



161
AKERNKLRFQ YKLDVWNHAH



 



181
ADMGITGTEI FYQTDKNIKL



 



201
DRNYKLRPED RYVQTERYGR



 



221
REIQKRYQHE LQAGSLLPDI



 



241
MIKTPKNPIH FVYRFAGDNY



 



261
ANKQFSEFEH TVKRRYGGET



 



281
EIKLKSKSGI MHDSKYLESW



 



301
ERGSADIRFA EFVGENRAHN



 



321
RQFPTATVNM GQQPDGQGGL



 



341
TRDRHVSVEF LMQSAPNSPW



 



361
AQALKKGELW DRVQLLARDG



 



381
NRYLSPHRLE YSDPEHFTEL



 



401
MNRVGLPASM GRQSHAASIK



 



421
FEKFDAQAAV IVINGPELRD



 



441
IHDLSPENLQ NVSTKDVIVA



 



461
DRNENGQRTG TYTSVAEYER



 



481
LQLRLPADAA GVLGEAADKY



 



501
SRDFVRPEPA SRPISDSRRI



 



521
YESRPRSQSV NSF*



 









SEQ ID NO:4












Amino acid sequence of virE3-pTi15955(1-2019)




Universal code



Total number of amino acids: 672, MW = 75584



Max ORF: 1-2016, 672 AA, MW = 75584



ORIGIN











1
MVSTTKKSFA KSLTADMRRS




 



21
AQRVVEQMRK ALITEEEALK



 



41
RQTRLESPDR KRKYAADMAI



 



61
VDKLDVGFRG EIGYKILGNK



 



81
RLRVDNPKEL TREHGRLRKT



 



101
KTVLKRNPVT QEVYLGLHER



 



121
KSWLSVSSHL YAADGTLRMK



 



141
HVKYKDGRFE ERWERDENGD



 



161
LIRTRYANRG RLFQPVSEKM



 



181
GAPYRSGPDN RLYRDLTRQN



 



201
GFRRETFERD DQGNLERIGS



 



221
NHVGFSKISV KAANRQTSQT



 



241
KIQKLGGAFN KSFRSLLDKE



 



261
GNELGRDILS HRRLYNKRSA



 



281
VYDEATGQLK SAKHTFGKIY



 



301
RSETDYLSAG LKKVSKKILG



 



321
VTVYRKFAAL SERESEAERL



 



341
RSFESGAHRQ IWQERAATPG



 



361
SPPSESDDIH FAQQSHLAKA



 



381
NSDHVEADVM RVTDQHIDVA



 



401
GQTSSSRQRN LEERLDSQSR



 



421
YKPANMLLSD PDLRADGPRP



 



441
YEGLAELTLR RDNESDGHKE



 



461
NDQRLRHFLQ PEPLVLPHPG



 



481
SPEITKVFGS RGEPLHPSGT



 



501
LHTAVGETAC EAPVMSSSLD



 



521
NHQPAPGQQE LLSLLHNAPA



 



541
PVSVAIHDEQ ERLAGEAPGG



 



561
SFRGSSGRTS SMSESIFDED



 



581
VQSHLVRDYS INPTNGFIDP



 



601
QSLFGGPDLS RGPKSGPEIP



 



621
SEDYHLSASE QENLLNQLLS



 



641
VPLPIPSPKP KSARSMIFEG



 



661
SRPRERSTSR GF*



 









SEQ ID NO:5












Derived amino acid sequence of




RSF1010_mobA(1-2130)



Universal code



Total number of amino acids: 709, MW = 77847











1
MAIYHLTAKT GSRSGGQSAR




 



21
AKADYIQREG KYARDMDEVL



 



41
HAESGHMPEF VERPADYWDA



 



61
ADLYERANGR LFKEVEFALP



 



81
VELTLDQQKA LASEFAQHLT



 



101
GAERLPYTLA IHAGGGENPH



 



121
CHLMISERIN DGIERPAAQW



 



141
FKRYNGKTPE KGGAQKTEAL



 



161
KPKAWLEQTR EAWADHANRA



 



181
LERAGHDARI DHRTLEAQGI



 



201
ERLPGVHLGP NVVEMEGRGI



 



221
RTDRADVALN IDTANAQIID



 



241
LQEYREAIDH ERNRQSEEIQ



 



261
RHQRVSGADR TAGPEHGDTG



 



281
RRSPAGHEPD PAGQRGAGGG



 



301
VAESPAPDRG GMGGAGQRVA



 



321
GGSRRGEQRR AERPERVAGV



 



341
ALEAMANRDA GFHDAYGGAA



 



361
DRIVALARPD ATDNRGRLDL



 



381
AALGGPMKND RTLQAIGRQL



 



401
KAMGCERFDI GVRDATTGQM



 



421
MNREWSAAEV LQNTPWLKRM



 



441
NAQGNPVYIR PAEQERHGLV



 



461
LVDDLSEFDL DDMKAEGREP



 



481
ALVVETSPKN YQAWVKVADA



 



501
AGGELRGQIA RTLASEYDAD



 



521
PASADSRHYG RLAGFTNRKD



 



541
KHTTRAGYQP WVLLRESKGK



 



561
TATAGPALVQ QAGQQIEQAQ



 



581
RQQEKARRLA SLELPERQLS



 



601
RHRRTALDEY RSEMAGLVKR



 



621
FGDDLSKCDF IAAQKLASRG



 



641
RSAEEIGKAM AEASPALAER



 



661
KPGHEADYIE RTVSKVMGLP



 



681
SVQLARAELA RAPAPRQRGM701 DRGGPDFSM*



 









SEQ ID NO:6












Translation of VirD5_pTi15955(1-2502)




Universal code



Total amino acid number: 833, MW = 92859











1
MTGKSKVHIR SSADTLPDGS




 



21
ITAPFSTGLS GDQADASFEA



 



41
QTDYSQSTSV SFTYDGVKLG



 



61
PAERAAYENW CEPGRPTWKD



 



81
LIIKARVDPI DDVIWLRDLE



 



101
EDTPSTFRYE GMPLGLGERK



 



121
AYENWQEDAQ PTWEDLVVSA



 



141
RMTELGRPHG ITGEYTSLAG



 



161
SKNTSSISLK RKRSNLTDDE



 



181
NSSGSFSYDG MKLGEAERSA



 



201
YGDWAEAEPP TWKDLVLRAR



 



221
VSSINDSAWL FDSQTSSSSF



 



241
EYNGVPLGEP ERQALRQWQG



 



261
DAQPTWEDLV VNARMAELCH



 



281
AGWIEGQKGC FEKRGEALHA



 



301
SERGSQRPIV QRTDSSDSFL



 



321
YDGRRLGAPE RTAYERWSKR



 



341
ERPTWEDLIL DAHQARIESD



 



361
AVTTQAIGQS SSLVFLYEGK



 



381
SLGCREREAY EKWRQPAQPR



 



401
WQNLVVNARL AELDPSVWIA



 



421
DERDPLDDGD ALGRPSYTSL



 



441
TDRSDVPLDD QSIYHRSDLV



 



461
REQVSESSQK QFAACSESET



 



481
IPVSWFTASG LDANNTENIA



 



501
ASDPVDGTGG VKRLGSKSDR



 



521
TVTASIHDVN SSTKRLLLNE



 



541
FGLEAPRPSP EKTVRLRSDN



 



561
IGTYGSRRNE RMRLATETGA



 



581
YESEHIFGFK AVHDTARATK



 



601
EGRRLERPMP AYLEYKGLHR



 



621
QHVGTGRGRT KLVGRGWPDD



 



641
TSYRSDQRAT LSDPVARSEG



 



661
ATASNGYQLN QLGYAHQLAS



 



681
DGLQSESPDG VALPIQVATT



 



701
SYNYTVSRDP VLVPPDKNEA



 



721
PQLLHLGPRG QTEAVLARET



 



741
ALTGKWPTLE REQQVYREFL



 



761
ALYDVKKDLE AKSVGVRQKK



 



781
KEVSSALDRT ARLIITSPSK



 



801
ARSEAETEKA IDELDDRRVY



 



821
DPRDRAQDKA FKR*













TABLE 2





Hand-alignment of C-terminal peptides
















(SEQ ID NO:25)










virF
EVMAEVRPIARSIKTAH DDARAELMSADRPRSTRGL*



 







(SEQ ID NO:26)








virE2
AADKYSRDFVRPEPASR PISDSRRIYESRPRSQSVNSF*


 







(SEQ ID NO:27)








virE3
LLNQLLSVPLPIPSPKP KSARSMIFEGSRPRERSTSRGF*


 







(SEQ ID NO:28)








VirD2
SASIGTEQPEASPKRPR DRHDGELGGRKRARGNRRDDGRGGT*


 







(SEQ ID NO:29)








VirD5
ITSPSKARSEAETEKAI DELDDRRVYDPRDRAQDKAFKR*


 







(SEQ ID NO:30)








mobA
YIERTVSKVMGLPSVQL ARAELARAPAPRQRGMDRGGPDFSM*

## Claims

1. A method of effecting a change in a cell, wherein a bacterial transfer system is contacted with the cell to be changed, said bacterial transfer system including a protein transport system comprising a pore comprising a VirB protein complex and a VirD4 coupling factor, wherein the bacterial transfer system comprises a fusion protein or is capable of making a fusion protein which is introduced into the cell to be changed using the protein transport system, the method comprising:
introducing the fusion protein into the cell to be changed, which fusion protein comprises a first part A and a second part B, the first part A and second part B derived from different proteins, wherein;
the first part A comprises an oligopeptide means for transporting part B through said pore, said means having the 20 most C-terminal amino acids of a bacterial protein transported through said pore, and at least two arginine or lysine amino acids and at least 50% hydrophilic or neutral amino acids; and
the second part B comprises a polypeptide capable of exerting a cell-changing activity in the cell to be changed,
wherein a C-terminal end of the polypeptide of the second part B is linked to an N-terminal end of the first part A, with the proviso that if the fusion protein comprises a first part A derived from VirE2, the fusion protein does not comprise the 84 N-terminal amino acids of VirE2; and
effecting a change in the cell.

2. The method according to claim 1, wherein the fusion protein is formed by expression in the bacterial transfer system.

3. The method according to claim 1, wherein the fusion protein is introduced into the cell to be changed without introducing a DNA- or RNA-sequence.

4. The method according to claim 2, wherein the fusion protein is introduced into the cell to be changed without introducing a DNA- or RNA-sequence.

5. The method according to claim 1, wherein the introduced fusion protein possesses a recombinase activity.

6. The method according to claim 2, wherein the introduced fusion protein possesses a recombinase activity.

7. The method according to claim 3, wherein the introduced fusion protein possesses a recombinase activity.

8. The method according to claim 4, wherein the introduced fusion protein possesses a recombinase activity.

9. The method according to claim 1, wherein a bacterium from the class of Rhizobiaceae is used as the transfer system.

10. The method according to claim 1, wherein the cell to be modified is selected from the group consisting of i) a plant cell; ii) a yeast cell; and iii) a fungal cell.

11. A vector that codes for a fusion protein BA, for use in a bacterial protein transport system comprising a pore and the fusion protein BA, wherein the pore comprises a VirB protein complex and a VirD4 coupling factor, the vector comprising:
a nucleic acid sequence coding for the fusion protein BA, wherein the nucleic acid sequence comprises a 5′ first part A linked to a 3′ second part B, wherein the first part A and the second part B encodes an amino acid sequence and the amino acid sequence of part A and part B are derived from different proteins, wherein:
the first part A encodes an oligopeptide means for transporting the 3′ second part B through the pore, said means comprising at least a 20 most C-terminal amino acid portion of a bacterial protein transported through said pore, and comprises at least two arginine or lysine amino acids and having at least 50% hydrophilic or neutral amino acids; and
the second part B encodes a polypeptide capable of effecting a cell-modifying activity in a cell to be modified, with the proviso that if the nucleic acid sequence comprises a first part A encoding at least the 20 most C-terminal amino acid portion of VirE2, the nucleic acid sequence does not encode a 84 most N-terminal amino acid portion of VirE2.

12. A vector set, comprising one or more vectors coding for a bacterial protein transport system, wherein the bacterial protein transport system comprises a fusion protein and a pore comprising a VirB protein complex and a VirD4 coupling factor, wherein the fusion protein comprises:
a first amino acid sequence at an N-terminal end of the fusion protein and a second amino acid sequence at a C-terminal end of the fusion protein, wherein the first amino acid sequence and the second amino acid sequence of the fusion protein are derived from different proteins, the first amino acid sequence being capable of exercising a cell-modifying activity in a cell to be modified; and
the second amino acid sequence comprising at least the 20 C-terminal amino acids of a bacterial protein, wherein the at least 20 C-terminal amino acids are a means for transporting the first amino acid sequence through the pore and comprises at least two arginine or lysine amino acids and at least 50% hydrophilic or neutral amino acids; with the proviso that if the at least 20 C-terminal amino acids are derived from VirE2, the fusion protein does not comprise a 84 most N-terminal amino acid region of VirE2.

13. The vector set of claim 12, wherein the second amino acid sequence comprises at least 20 amino acids selected from the group consisting of at least the 20 most C-terminal amino acids of VirF, VirD2, VirE2, VirE3, VirD5 and MobA.

14. The method according to claim 1, wherein the bacterial protein transported through said pore is selected from the group consisting of VirF, VirD2, VirE2, VirE3, VirD5 and MobA.

15. The vector of claim 11, wherein the bacterial protein transported through said pore is selected from the group consisting of VirF, VirD2, VirE2, VirE3, VirD5 and MobA.

16. The vector set of claim 12, wherein the bacterial protein transported through said pore is selected from the group consisting of VirF, VirD2, VirE2, VirE3, VirD5 and MobA.