# Patent

## Title
Optimized endonucleases and uses thereof

## Abstract

Provided are optimized endonucleases, as well as methods of targeted integration, targeted deletion or targeted mutation of [polynucleotides using optimized endonucleases.

## Background
RELATED APPLICATIONS
This application is a national stage application (under 35 U.S.C. §371) of PCT/AB2010/055428, filed Nov. 25, 2010 which claims benefit of U.S. Provisional Application No. 61/264,715, filed Nov. 27, 2009, European Application No. 09177375.4, filed Nov. 27, 2009; U.S. Provisional Application No. 61/365,836, filed Jul. 20, 2010, and European Application No. 10170199.3, filed Jul. 20, 2010.
SUBMISSION OF SEQUENCE LISTING
The Sequence Listing associated with this application is filed in electronic format via EFS-Web and hereby incorporated by reference into the specification in its entirety. The name of the text file containing the Sequence Listing is Revised Sequence Listing 13987 00192 US. The size of the text file is 108 KB and the text file was created on Apr. 10, 2013.


FIELD OF THE INVENTION
The invention relates to optimized endonucleases, as well as methods of targeted integration, targeted deletion or targeted mutation of polynucleotides using optimized endonucleases.
BACKGROUND OF THE INVENTION
Genome engineering is a common term to summarize different techniques to insert, delete, substitute or otherwise manipulate specific genetic sequences within a genome and has numerous therapeutic and biotechnological applications. More or less all genome engineering techniques use recombinases, integrases or endonucleases to create DNA double strand breaks at predetermined sites in order to promote homologous recombination.
In spite of the fact that numerous methods have been employed to create DNA double strand breaks, the development of effective means to create DNA double strand breaks at higly specific sites in a genome remains a major goal in gene therapy, agrotechnology, and synthetic biology.
One approach to achieve this goal is to use nucleases with specificity for a sequence that is sufficiently large to be present at only a single site within a genome. Nucleases recognizing such large DNA sequences of about 15 to 30 nucleotides are therefore called “meganucleases” or “homing endonucleases” and are frequently associated with parasitic or selfish DNA elements, such as group 1 self-splicing introns and inteins commonly found in the genomes of plants and fungi. Meganucleases are commonly grouped into four families: the LAGLIDADG family, the GIY-YIG family, the His-Cys box family and the HNH family. These families are characterized by structural motifs, which affect catalytic activity and the sequence of their DNA recognition sequences.
Natural meganucleases from the LAGLIDADG family have been used to effectively promote site-specific genome modifications in insect and mammalian cell cultures, as well as in many organisms, such as plants, yeast or mice, but this approach has been limited to the modification of either homologous genes that conserve the DNA recognition sequence or to preengineered genomes into which a recognition sequence has been introduced. In order to avoid these limitations and to promote the systematic implementation of DNA double strand break stimulated gene modification new types of nucleases have been created.
One type of new nucleases consists of artificial combinations of unspecific nucleases to a higly specific DNA binding domain. The effectiveness of this strategy has been demonstrated in a variety of organisms using chimeric fusions between an engineered zinc finger DNA-binding domain and the non-specific nuclease domain of the FokI restriction enzyme (e.g. WO03/089452) a variation of this approach is to use an inactive variant of a meganuclease as DNA binding domain fused to an unspecific nuclease like Fokl as disclosed in Lippow et al., “Creation of a type IIS restriction endonuclease with a long recognition sequence”, Nucleic Acid Research (2009), Vol. 37, No. 9, pages 3061 to 3073.
An alternative approach is to genetically engineer natural meganucleases in order to customize their DNA binding regions to bind existing sites in a genome, thereby creating engineered meganucleases having new specificities (e.g WO07093918, WO2008/093249, WO09114321). However, many meganucleases which have been engineered with respect to DNA cleavage specificity have decreased cleavage activity relative to the naturally occurring meganucleases from which they are derived (US2010/0071083). Most meganucleases do also act on sequences similar to their optimal binding site, which may lead to unintended or even detrimental off-target effects. Several approaches have already been taken to enhance the efficiency of meganuclease induced homologous recombination e.g. by fusing nucleases to the ligand binding domain of the rat Glucocorticoid Receptor in order to promote or even induce the transport of this modified nuclease to the cell nucleus and therefore its target sites by the addition of dexamethasone or similar compounds (WO2007/135022). Despite that fact, there is still a need in the art to develop meganucleases having high induction rates of homologous recombination and/or a high specificity for their binding site, thereby limiting the risk of off-target effects.
BRIEF SUMMARY OF THE INVENTION
The invention provides optimized versions of endonucleases of the LAGLIDADG endonuclease family. In particular optimized endonucleases comprising an amino acid sequence having at least 80% amino acid sequence identity to a polypeptide described by SEQ ID NO: 1, 15, 16, 17 or 19. In one embodiment of the invention, the optimized endonucleases are wildtype or engineered versions of I-SceI, as described by SEQ ID NO: 1 or one of its homologs having at least 55%, 58%, 60%, 70%, 80%, 85%, 90%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% sequence identity on amino acid level, having one or more mutations selected from the groups of:
a) I-SceI-1, I-SceI-2, I-SceI-3, I-SceI-4, I-SceI-5, I-SceI-6, I-SceI-7, I-SceI-8 and I-SceI-9;
b) S229K, S229A, S229P, S229G, S229E, S229Q, S229D, S229N, S229C, S229Y, S229T, M203K, M203H, M203R, Q77K, Q77H, Q77R, E130K, E130H, E130R, Y199K, Y199H and Y199R;
c) a methionine, valine, glycine, threonin, serine, alanine, cysteine, glutamic acid, glutamine, aspartic acid, asparagine, isoleucine or histidine after the start methionine of their amino acid sequence; or
d) a combination of one or more mutations selected from a) and b), a) and c), b) and c) or a) b) and c) above.
In one embodiment of the invention, the optimized endonuclease comprises an amino acid sequence described by SEQ ID NO 2, 3 or 5.
In a further embodiment of the invention, the optimized endonucleases is an engineered version of an endonuclease comprising an amino acid sequence having at least 80% amino acid sequence identity to a polypeptide described by SEQ ID NO: 1, 15, 16, 17 or 19.
In another embodiment, the invention provides an endonuclease having at least 80% amino acid sequence identity to a polypeptide described by SEQ ID NO: 1, or an engineered version of an endonuclease having at least 80% amino acid sequence identity to a polypeptide described by SEQ ID NO: 1, wherein the amino acid sequence TISSETFLK is removed by deletion or mutation of any one of the amino acids of the amino acid sequence TISSETFLK. Another preferred embodiment of the invention is an optimized endonuclease as claimed in any of claims 1 to 4 comprising an amino acid sequence having at least 80% amino acid sequence identity to a polypeptide described by SEQ ID NO: 1 or 2 and comprising a mutation of serine Nr 229 of SEQ ID NO: 1. In a further embodiment of the invention, the optimized endonuclease is fused to at least one zinc finger domain, or a at least one repeat units derived from a transcription activator-like (TAL) effector, or at least one zinc finger domain and at least one repeat units derived from a transcription activator-like (TAL) effector. Preferably the optimized endonucleases comprise an SceIII or SecIV secretion signal. The invention does also provide isolated polynucleotides comprising a polynucleotide sequence, which codes for an optimized endonuclease.
Preferably this polynucleotide is codon opitimized or has a low content RNA instability motives or has a low content of codon repeats, or has a low content of cryptic splice sites, or has a low content of alternative start codons, has a low content of restriction sites, or has a low content of RNA secondary structures or has any combination of the features described above. Another embodiment of the invention is an expression cassette comprising an isolated polynucleotide as described above in functional combination with a promoter and a terminator sequence. Other embodiments of the invention are vectors, host cells or non human organisms comprising a polynucleotide coding for an optimized endonuclease, or an isolated polynucleotide coding for an optimized endonuclease, or an expression cassette comprising a polynucleotide coding for an optimized endonuclease, and vectors, host cells or non human organisms comprising a combination of the endonucleoases, polynucleotides and expression cassettes described above. Preferably the non human organism is a plant.
The invention provides methods of using the endonucleases described herein to induce homologous recombination or end joining events. Preferably in methods for targeted integration of excision of sequences. Preferably the sequences being excised are marker genes. The invention does further provide a method for homologous recombination of polynucleotides comprising the following steps: a) providing a cell competent for homologous recombination, b) providing a polynucleotide comprising a DNA recognition site of an optimized endonuclease flanked by a sequence A and a sequence B, c) providing a polynucleotide comprising sequences A′ and B′, which are sufficiently long and homologous to sequence A and sequence B, to allow for homologous recombination in said cell and d) providing an optimized endonuclease as described herein or an expression cassette as described herein, e) combining b), c) and d) in said cell and f) detecting recombined polynucleotides of b) and c), or selecting for or growing cells comprising recombined polynucleotides of b) and c). Preferably the method for homologous recombination of polynucleotides leads to a homologous recombination, wherein a polynucleotide sequence comprised in the competent cell of step a) is deleted from the genome of the growing cells of step f). A further method of the invention is a method for targeted mutation comprising the following steps: a) providing a cell comprising a polynucleotide comprising a DNA recognition site of an optimized endonuclease, b) providing an optimized endonuclease as claimed in any one of claims 1 to 7 or an expression cassette as claimed in claim 10 and being able to cleave the DNA recognition site of step a), c) combining a) and b) in said cell and d) detecting mutated polynucleotides, or selecting for or growing cells comprising mutated polynucleotides.
In another preferred embodiment of the invention, the methods described above comprise a step, wherein the optimized endonuclease and the DNA recogntition site are combined in at least one cell via crossing of organisms, via transformation or via transport mediated via a Sec III or SecIV peptide fused to the optimized endonuclease.



BRIEF DESCRIPTION OF THE FIGURES
FIG. 1 shows a comparison of the frequency of homologous recombination, measured by restoration of beta glucuronidase activity (% blue seedlings), after induced recombination by three different I-SceI variants. Each I-SceI variant was tested in five different plant lines, carrying the test construct. For each combination 96 seedlings of the T2 generation were analyzed for beta glucuronidase activity (“I-SceI”, having the amino acid sequence described by SEQ ID NO: 1; “I-SceI c-term mod” having the amino acid sequence described by SEQ ID NO: 3; “NLS I-SceI c-term mod”, having the amino acid sequence described by SEQ ID NO: 5), see also Example 10b.
FIG. 2 depicts a sequence alignment of different I-SceI homologs, wherein 1 is SEQ ID NO: 1, 2 is SEQ ID NO: 15, 3 is SEQ ID NO: 16, 4 is SEQ ID NO: 17, 5 is SEQ ID NO: 18 and Consensus is SEQ ID NO: 43).



DESCRIPTION OF THE INVENTION
The invention provides optimized endonucleases, which can be used as alternative DNA double strand break inducing enzymes. The invention does also provide methods of using these optimized endonucleases.
Optimized endonucleases are variants of I-Sce-I (described by SEQ ID NO: 1) and homologs of I-Sce I having at least 55%, 58%, 60%, 70%, 80%, 85%, 90%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% sequence identity on amino acid level. Optimized versions of I-SceI are also called optimized I-SceI.
Homologs of I SceI endonucleases can be cloned from other organisms or can be created by mutating LAGLIDADG endonucleases, e.g. by replacing, adding or deleting amino acids of the amino acid sequence of a given LAGLIDADG endonuclease.
For example, it is possible to add nuclear localization signals to the amino acid sequence of a LAGLIDADG endonuclease and/or change one or more amino acids and/or to delete parts of its sequence, e.g. parts of the N-terminus or parts of its C-terminus.







TABLE 1







Exemplary homologs of I-Scel, which can be cloned


from other organisms are described in Table 1;










Uni-Prot

SEQ
Amino Acid


Accession Nr.
Organism
ID NO:
Sequence Identity to I-Scel













A7LCP1
S. cerevisiae
1
100


Q36760
S. cerevisiae
15
98


O63264
Z. bisporus
16
72


Q34839
K. thermotolerans
17
71


Q34807
P. canadensis
18
58









LAGLIDADG endonucleases usefull in the invention can be found in the genomes of algae, fungi, yeasts, protozoan, chloroplasts, mitochondria, bacteria and archaea. LAGLIDADG endonucleases comprise at least one conserved LAGLIDADG motif (SEQ ID NO: 32). The name of the LAGLIDADG motif (SEQ ID NO: 32) is based on a characteristic amino acid sequence appearing in all LAGLIDADG endonucleases. The term LAGLIDADG is an acronym of this amino acid sequence according to the one-letter-code as described in the STANDARD ST.25 i.e. the standard adopted by the PCIPI Executive Coordination Committee for the presentation of nucleotide and amino acid sequence listings in patent applications.
However, the LAGLIDADG motif SEQ ID NO: 32) is not fully conserved in all LAGLIDADG endonucleases, (see for example Chevalier et al. (2001), Nucleic Acids Res. 29(18): 3757 to 3774, or Dalgaard et al. (1997), Nucleic Acids Res. 25(22): 4626 to 4638), so that some LAGLIDADG endonucleases comprise some one or several amino acid changes in their LAGLIDADG motif (SEQ ID NO: 32). LAGLIDADG endonucleases comprising only one LAGLIDADG motif (SEQ ID NO: 32) act usually as homo- or heterodimers. LAGLIDADG endonucleases comprising two LAGLIDADG motifs (SEQ ID NO: 32) act as monomers and comprise usually a pseudo-dimeric structure.
LAGLIDADG endonucleases can be isolated from polynucleotides of organisms mentioned as examples in Table 1, or de novo synthesized by techniques known in the art, e.g. using sequence information available in public databases known to the person skilled in the art, for example Genbank (Benson (2010)), Nucleic Acids Res 38:D46-51 or Swissprot (Boeckmann (2003), Nucleic Acids Res 31:365-70)
A collection of LAGLIDADG endonucleases can be found in the PFAM-Database for protein families. The PFAM-Database accession number PF00961 describes the LAGLIDADG 1 protein family, which comprises about 800 protein sequences. PFAM-Database accession number PF03161 describes members of the LAGLIDADG 2 protein family, comprising about 150 protein sequences. An alternative collection of LAGLIDADG endonucleases can be found in the InterPro data base, e.g. InterPro accession number IPR004860.
Another way to create homologs of LAGLIDADG endonucleases is to mutate the amino acid sequence of an LAGLIDADG endonuclease in order to modify its DNA binding affinity, its dimer formation affinity or to change its DNA recognition sequence. The determination of protein structure as well as sequence alignments of homologs of LAGLIDADG endonucleases allows for rational choices concerning the amino acids that can be changed to affect its DNA binding affinity, its enzymatic activity, or to change its DNA recognition sequence.
As used herein, the term “DNA-binding affinity” means the tendency of a meganuclease or LAGLIDADG endonuclease to non-covalently associate with a reference DNA molecule (e.g., a DNA recognition sequence or an arbitrary sequence). Binding affinity is measured by a dissociation constant, KD (e.g., the KD of I-SceI for the WT DNA recognition sequence is approximately 0.1 nM). As used herein, a meganuclease has “altered” binding affinity if the KD of the recombinant meganuclease for a reference DNA recognition sequence is increased or decreased by a statistically significant (p<0.05) amount relative to a reference meganuclease or or LAGLIDADG endonuclease.
As used herein, the term “enzymatic activity” refers to the rate at which a meganuclease e.g. a LAGLIDADG endonuclease cleaves a particular DNA recognition sequence. Such activity is a measurable enzymatic reaction, involving the hydrolysis of phospho-diester-bonds of double-stranded DNA. The activity of a meganuclease acting on a particular DNA substrate is affected by the affinity or avidity of the meganuclease for that particular DNA substrate which is, in turn, affected by both sequence-specific and non-sequence-specific interactions with the DNA.
Nucleases may further be optimized by deleting 50, 40, 30, 20, 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 amino acids of its amino acid sequence, without destroying its endonuclease activity. For example, in case parts of the amino acid sequence of a LAGLIDADG endonuclease is deleted, it is important to retain the LAGLIDADG endonuclease motif described above.
It is preferred to delete PEST sequences or other destabilizing motifs like KEN-box, D-box and A-box. Those motifs can also be destroyed by indroduction of single amino acid exchanges, e.g introduction of a positively charged aminoacid (arginine, histidine and lysine) into the PEST sequence.
LAGLIDADG endonucleases, which have been mutated in order to modify their DNA binding affinity, or to change its DNA recognition sites are called engineered endonucleases. I-SceI as well as homologs of I-Sce I having at least 55%, 58%, 60%, 70%, 80%, 85%, 90%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% sequence identity on amino acid level can be engineered like other LAGLIDADG endonucleases in order to change its DNA binding affinity, its enzymatic activity, or to change its DNA recognition sequence. Engineered versions of I-SceI and homologs of I-Sce I having at least 55%, 58%, 60%, 70%, 80%, 85%, 90%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% sequence identity on amino acid level.
Accordingly in one embodiment of the invention, the optimized endonucleases are engineered version of I-SceI or its homologs having at least 55%, 58%, 60%, 70%, 80%, 85%, 90%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% sequence identity on amino acid level and having a changed DNA binding affinity, a changed enzymatic activity, or a changed DNA recognition sequence, when compared to its non engineered form, meaning the respective LAGLIDADG endonuclease at it occurs in nature.
In another embodiment of the invention, the optimized endonucleases are variants of I-SceI as described by SEQ ID NO: 1 or its homologs having at least 55%, 58%, 60%, 70%, 80%, 85%, 90%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% sequence identity on amino acid level like they occure in nature.
Homologs, which do not occure in nature, but have at least one of the mutations A36G, L40M, L40V, I41S, I41N, L43A, H91A and I123L, which have little effect on the DNA binding affinity of I-SceI, or will change its DNA recognition sequence will also be considered to be homologs occurring in nature, as long as they do not comprise other mutations, which change their DNA binding affinity, their enzymatic activity, or their DNA recognition sequence, when compared to I-SceI as described by SEQ ID NO: 1 or the respective homolog having at least 55%, 58%, 60%, 70%, 80%, 85%, 90%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% sequence identity on amino acid level like it occures in nature.
Engineered versions of I-SceI, having an increased or decreased DNA-binding affinity are for example disclosed in WO07/047859 and WO09/076292 herein included by reference.
If not explicitly mentioned otherwise, all mutants will be named according to the amino acid numbers of the wildtype amino acid sequences of the respective endonuclease, e.g. the mutant L19 of I-SceI will have an amino acid exchange of leucine at position 19 of the wildtype I-SceI amino acid sequence, as described by SEQ ID NO: 1. The L19H mutant of I-SceI, will have a replacement of the amino acid leucine at position 19 of the wildtype I-SceI amino acid sequence with hystidine.
For example, the DNA-binding affinity of I-SceI can be increased by at least one modification corresponding to a substitution selected from the group consisting of:

    (a) substitution of D201, L19, L80, L92, Y151, Y188, I191, Y199 or Y222 with H, N, Q, S, T, K or R; or
    (b) substitution of N15, N17, S81, H84, N94, N120, T156, N157, S159, N163, Q165, S166, N194 or S202 with K or R.


DNA-binding affinity of I-SceI can be decreased by at least one mutation corresponding to a substitution selected from the group consisting of:

    (a) substitution of K20, K23, K63, K122, K148, K153, K190, K193, K195 or K223 with H, N, Q, S, T, D or E; or
    (b) substitution of L19, L80, L92, Y151, Y188, 1191, Y199, Y222, N15, N17, S81, H84, N94, N120, T156, N157, S159, N163, Q165, S166, N194 or S202 with D or E.


Engineered versions of I-SceI, I-CreI, I-MsoI and I-CeuI having a changed DNA recognition sequence are disclosed for example in WO007/047859 and WO09/076292.
For example, an important DNA recognition site of I-SceI has the following sequence:









sense:
5′-T T A C C C T G T  T  A  T  C  C  C  T  A  G-3′




(SEQ ID NO: 44)


base position:
   1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18


antisense
3′-A A T G G G A C A  A  T  A  G  G  G  A  T  C-5′



(SEQ ID NO: 45)






The following mutations of I-SceI will change the preference for C at position 4 to A: K50
The following mutations of I-SceI will keep the preference for C at position 4: K50, CE57
The following mutations of I-SceI will change the preference for C at position 4 to G: E50, R57, K57.
The following mutations of I-SceI will change the preference for C at position 4 to T: K57, M57, Q50.
The following mutations of I-SceI will change the preference for C at position 5 to A: K48, Q102.
The following mutations of I-SceI will keep the preference for C at position 5: R48, K48, E102, E59
The following mutations of I-SceI will change the preference for C at position 5 to G: E48, K102, R102.
The following mutations of I-SceI will change the preference for C at position 5 to T: Q48, C102, L102, V102.
The following mutations of I-SceI will change the preference for C at position 6 to A: K59.
The following mutations of I-SceI will keep the preference for C at position 6: R59, K59.
The following mutations of I-SceI will change the preference for C at position 6 to G: K84, E59.
The following mutations of I-SceI will change the preference for C at position 6 to T: Q59, Y46.
The following mutations of I-SceI will change the preference for T at position 7 to A: C46, L46, V46.
The following mutations of I-SceI will change the preference for T at position 7 to C: R46, K46, E86.
The following mutations of I-SceI will change the preference for T at position 7 to G: K86, R86, E46.
The following mutations of I-SceI will keep the preference for T at position 7: K68, C86, L86, Q46*.
The following mutations of I-SceI will change the preference for G at position 8 to A: K61, S61, V61, A61, L61.
The following mutations of I-SceI will change the preference for G at position 8: E88, R61, H61.
The following mutations of I-SceI will keep the preference for G at position 8: E61, R88, K88.
The following mutations of I-SceI will change the preference for G at position 8 to T: K88, Q61, H61.
The following mutations of I-SceI will change the preference for T at position 9 to A: T98, C98, V98, L9B.
The following mutations of I-SceI will change the preference for T at position 9 to C: R98, K98.
The following mutations of I-SceI will change the preference for T at position 9 to G: E98, D98.
The following mutations of I-SceI will keep the preference for T at position 9: Q98.
The following mutations of I-SceI will change the preference for T at position 10 to A: V96, C96, A96.
The following mutations of I-SceI will change the preference for T at position 10 to C: K96, R96.
The following mutations of I-SceI will change the preference for T at position 10 to G: D96, E96.
The following mutations of I-SceI will keep the preference for T at position 10: Q96.
The following mutations of I-SceI will keep the preference for A at position 11: C90, L90.
The following mutations of I-SceI will change the preference for A at position 11 to C: K90, R90.
The following mutations of I-SceI will change the preference for A at position 11 to G: E90.
The following mutations of I-SceI will change the preference for A at position 11 to T: Q90.
The following mutations of I-SceI will change the preference for T at position 12 to A: 0193.
The following mutations of I-SceI will change the preference for T at position 12 to C: E165, E193, D193.
The following mutations of I-SceI will change the preference for T at position 12 to G: K165, R165.
The following mutations of I-SceI will keep the preference for T at position 12: C165, L165, C193, V193, A193, T193, S193.
The following mutations of I-SceI will change the preference for C at position 13 to A: C193, L193.
The following mutations of I-SceI will keep the preference for C at position 13: K193, R193, D192.
The following mutations of I-SceI will change the preference for C at position 13 to G: E193, D193, K163, R192.
The following mutations of I-SceI will change the preference for C at position 13 to T: Q193, C163, L163.
The following mutations of I-SceI will change the preference for C at position 14 to A: L192, C192.
The following mutations of I-SceI will keep the preference for C at position 14: E161, R192, K192.
The following mutations of I-SceI will change the preference for C at position 14 to G: K147, K161, R161, R197, D192, E192.
The following mutations of I-SceI will change the preference for C at position 14 to T: K161, Q192.
The following mutations of I-SceI will keep the preference for C at position 15: E151.
The following mutations of I-SceI will change the preference for C at position 15 to G: K151.
The following mutations of I-SceI will change the preference for C at position 15 to T: C151, L151, K151.
The following mutations of I-SceI will keep the preference for A at position 17: N152, S152, C150, L150, V150, T150.
The following mutations of I-SceI will change the preference for A at position 17 to C: K152, K150.
The following mutations of I-SceI will change the preference for A at position 17 to G: N152, S152, D152, D150, E150.
The following mutations of I-SceI will change the preference for A at position 17 to T: Q152, Q150.
The following mutations of I-SceI will change the preference for G at position 18 to A: K155, C155.
The following mutations of I-SceI will change the preference for G at position 18: R155, K155.
The following mutations of I-SceI will keep the preference for G at position 18: E155.
The following mutations of I-SceI will change the preference for G at position 18 to T: H155, Y155.
Combinations of several mutations may enhance the effect. One example is the triple mutant W149G, D150C and N152K, which will change the preference of I-SceI for A at position 17 to G.
In order to preserve the enzymatic activity the mutations 138S, 138N, G39D, G39R, L40Q, L42R, D44E, D44G, D44H, D44S, A45E, A45D, Y46D, 147R, 147N, D144E, D145E, D145N and G146E of I-SceI or its homolog having at least 55%, 58%, 60%, 70%, 80%, 85%, 90%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% sequence identity on amino acid level, should be avoided.
Mutations which alter the enzymatic activity, the DNA-binding-affinity, the DNA recognition sequence of I-SceI or its homolog having at least 55%, 58%, 60%, 70%, 80%, 85%, 90%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% sequence identity on amino acid level may be combined to create an engineered endonuclease, e.g. an engineered endonuclease based on I-SceI and having an altered DNA-binding-affinity and/or a changed DNA recognition sequence, when compared to I-SceI as described by SEQ ID NO: 1.
Besides rational engineering of I-SceI, it is also possible to alter the enzymatic activity, the DNA-binding-affinity, the DNA recognition sequence of I-SceI or its homolog having at least 55%, 58%, 60%, 70%, 80%, 85%, 90%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% sequence identity on amino acid level, by employing molecular evolution. Polynucleotides encoding a candidate endonuclease enzyme can, for example, be modulated with DNA shuffling protocols. DNA shuffling is a process of recursive recombination and mutation, performed by random fragmentation of a pool of related genes, followed by reassembly of the fragments by a polymerase chain reaction-like process. See, e.g., Stemmer (1994) Proc Natl Acad Sci USA 91:10747-10751; Stemmer (1994) Nature 370:389-391; and U.S. Pat. Nos. 5,605,793, 5,837,458, 5,830,721 and 5,811,238. Engineered endonucleases can also be created by using rational design, based on further knowledge of the crystal structure of a given endonuclease see for example Fajardo-Sanchez et al., Computer design of obligate heterodimer meganucleases allows efficient cutting of custom DNA sequences, Nucleic Acids Research, 2008, Vol. 36, No. 7 2163-2173.
Numerous examples of engineered endonucleases, as well as their respective DNA recognition sites are known in the art and are disclosed for example in: WO 2005/105989, WO 2007/034262, WO 2007/047859, WO 2007/093918, WO 2008/093249, WO 2008/102198, WO 2008/152524, WO 2009/001159, WO 2009/059195, WO 2009/076292, WO 2009/114321, or WO 2009/134714, WO 10/001189 herein included by reference.
Mutations and changes in order to create optimized nucleases may be combined with the mutations used to create engineered endonucleases, for example, a homologue of I-SceI may be an optimized nuclease as described herein, but may also comprise mutations used to alter its DNA-binding-affinity and/or change its DNA recognition sequence.
The amino acid sequence of I-SceI or its homologs having at least 55%, 58%, 60%, 70%, 80%, 85%, 90%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% sequence identity on amino acid level, as well as the polynucletides coding for I-SceI or its homologs having at least 55%, 58%, 60%, 70%, 80%, 85%, 90%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% sequence identity on amino acid level, can be improved by adapting the polynucleotide sequence to the codon usage of the organism, in which I-SceI or its homologs having at least 55%, 58%, 60%, 70%, 80%, 85%, 90%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% sequence identity on amino acid level is intended to be expressed, or by deleting alternative start codons, or by deleting cryptic polyadenylation signals from the polynucleotide sequence coding for the endonuclease
Mutations Used to Create Optimized Nucleases:
Optimized nucleases like optimized versions of I-SceI or its homologs having at least 55%, 58%, 60%, 70%, 80%, 85%, 90%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% sequence identity on amino acid level can be optimized by changing the amino acid sequence of the respective LAGLIDADG endonuclease to enhance protein stability. Accordingly optimized nucleases do not comprise or have a reduced number compared to the amino acid sequence of the non optimized nuclease of:
a) PEST-Sequences,
b) KEN-boxes
c) A-boxes,
d) D-boxes, or
e) do comprise an optimized N-terminal end for stability according to the N-end rule,
f) comprise a glycin as the second N-terminal amino acid, or
g) any combination of a), b), c) d), e) and f).
PEST Sequences are sequences of about 12 amino acids, comprising at least one prolin, one glutamate or aspartate and at least one serin or threonine. PEST Sequences are for example described in Rechsteiner M, Rogers SW. “PEST sequences and regulation by proteolysis.”Trends Biochem, Sci. 1996; 21(7), pages 267 to 271.
The amino acid consensus sequence of a KEN-box is: KENXXX(N/D)
The amino acid consensus sequence of a A-box is: AQRXLXXSXXXQRVL (SEQ ID NO: 33)
The amino acid consensus sequence of a D-box is: RXXL
A further way to stabilize nucleases against degradation is to optimize the amino acid sequence of the N-terminus of the respective endonuclease according to the N-end rule. Nucleases which are optimized for the expression in eucaryotes comprise either methionine, valine, glycine, threonine, serine, alanine or cysteine after the start methionine of their amino acid sequence. Nucleases which are optimized for the expression in procaryotes comprise either methionine, valine, glycine, threonine, serine, alanine, cysteine, glutamic acid, glutamine, aspartic acid, asparagine, isoleucine or histidine after the start methionine of their amino acid sequence.
Nucleases may further be optimized by deleting 50, 40, 30, 20, 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 amino acids of its amino acid sequence, without destroying its endonuclease activity. For example, in case parts of the amino acid sequence of a LAGLIDADG endonuclease is deleted, it is important to retain the LAGLIDADG endonuclease motif (SEQ ID NO: 32) described above.
Another way to optimize nucleases is to add nuclear localization signals to the amino acid sequence of the nuclease. For example a nuclear localization signal as described by SEQ ID NO: 4.
Optimized nucleases may comprise a combination of the methods and features described above, e.g. they may comprise a nuclear localization signal, comprise a glycin as the second N-terminal amino acid or a deletion at the C-terminus or a combination of these features. Examples of optimized nucleases having a combination of the methods and features described above are for example described by SEQ ID NOs: 2, 3 and 5.
Optimized nucleases do not comprise an amino acid sequence described by the sequence:
HVCLLYDQWVLSPPH (SEQ ID NO: 25), LAYWFMDDGGK (SEQ ID NO: 26), KTIPNNLVENYLTPMSLAYWFMDDGGK (SEQ ID NO: 27), KPIIYIDSMSYLIFYNLIK (SEQ ID NO: 28), KLPNTISSETFLK (SEQ ID NO: 29), or TISSETFLK (SEQ ID NO: 31),
or which does not comprise an amino acid sequence described by the sequence: HVCLLYDQWVLSPPH (SEQ ID NO: 25), LAYWFMDDGGK (SEQ ID NO: 26), KPIIYIDSMSYLIFYNLIK (SEQ ID NO: 28), KLPNTISSETFLK (SEQ ID NO: 29) or TISSETFLK (SEQ ID NO: 31),
or which does not comprise an amino acid sequence described by the sequence: HVCLLYDQWVLSPPH (SEQ ID NO: 25), LAYWFMDDGGK (SEQ ID NO: 26), KLPNTISSETFLK (SEQ ID NO: 28) or TISSETFLK (SEQ ID NO: 31), or which does not comprise an amino acid sequence described by the sequence: LAYWFMDDGGK (SEQ ID NO: 26), KLPNTISSETFLK (SEQ ID NO: 28) or TISSETFLK (SEQ ID NO: 31),
or which does not comprise an amino acid sequence described by the sequence: KLPNTISSETFLK (SEQ ID NO: 28) or TISSETFLK (SEQ ID NO: 31).
In one embodiment the optimized nuclease is I-SceI, or its homologs having at least 55%, 58%, 60%, 70%, 80%, 85%, 90%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% sequence identity on amino acid level in which the amino acid sequence TISSETFLK at the C-terminus of wildtype I-SceI or its homologs having at least 55%, 58%, 60%, 70%, 80%, 85%, 90%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% sequence identity on amino acid level and having an amino acid sequence TISSETFLK (SEQ ID NO: 31) at the C-terminus is deleted or mutated.
The amino acid sequence TISSETFLK (SEQ ID NO: 31) may be deleted or mutated, by deleting or mutating at least 1, 2, 3, 4, 5, 6. 7, 8 or 9 amino acids of the C-terminus of wildtype I-Scel or its homologs having at least 55%, 58%, 60%, 70%, 80%, 85%, 90%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% sequence identity on amino acid level and having an amino acid sequence TISSETFLK (SEQ ID NO: 31) at the C-terminus.







TABLE 2







Different examples for deletions of the TISSETFLK


(SEQ ID NO: 31) amino acid sequence in wildtype I-Scel








Wildtype and optimized I-Scel
amino acid sequence on C-terminus





I-Scel wildtype
TISSETFLK (SEQ ID NO: 31)


I-Scel -1
TISSETFL (SEQ ID NO: 34)


I-Scel -2
TISSETF (SEQ ID NO: 35)


I-Scel -3
TISSET (SEQ ID NO: 36)


I-Scel -4
TISSE (SEQ ID NO: 37)


I-Scel -5
TISS (SEQ ID NO: 38)


I-Scel -6
TIS


I-Scel -7
TI


I-Scel -8
T


I-Scel -9
complete deletion









In one embodiment of the invention, the optimized nucleases or optimized versions of I-Scel and its homologs having at least 55%, 58%, 60%, 70%, 80%, 85%, 90%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% sequence identity on amino acid level comprise at least one of the following mutations: L74K, Y75H, Q77K, E130K, T134H, Y199H, M203K, Y205H.
Equally preferred, is to mutate serine at position 229 of the amino acid sequence of wildtype I-SceI as disclosed in SEQ ID NO: 1 to Lys, Ala, Pro, Gly, Glu, GIn, Asp, Asn, Cys, Tyr or Thr. Thereby creating the I-SceI mutants S229K, S229A, S229P, S229G, S229E, S229Q, S229D, S229N, S229C, S229Y, or S229T. Amino acid No. 229 of wildtype I-SceI is amino acid Nr. 230 in SEQ ID NO: 2.
In another embodiment of the invention, the amino acid methionine at position 202 of the amino acid sequence of wildtype I-SceI as disclosed in SEQ ID No. 1 (being amino acid 203 if referenced to SEQ ID No. 2), is mutated to Lys, His or Arg. Thereby creating the I-SceI mutant M202K, M202H and M202R.
Alternatively the amino acid sequence TISSETFLK (SEQ ID NO: 31) may be mutated, e.g. to the amino acid sequence: TIKSETFLK (SEQ ID NO: 39), or AIANQAFLK ESEQ ID NO: 40).
Preferred optimized versions of I-SceI are the deletions I-SceI -1, I-SceI -2, I-SceI -3, I-SceI -4, I-SceI -5, I-SceI -6, I-SceI -7, I-SceI -8, I-SceI -9 and the mutants S229K and S229A, even more preferred are the deletions I-SceI -1, I-SceI -2, I-SceI -3, I-SceI -4, I-SceI -5, I-SceI -6 and the mutant S229K. Most preferred are the deletion I-SceI -5 (SEQ ID NO: 30) and the mutant S229K.
It is also possible to combine the deletions and mutations described above, e.g. by combining the deletion I-SceI -1 with the mutant S229A, thereby creating the amino acid sequence TIASETFL (SEQ ID NO: 41) at the C-terminus.
Further preferred optimized versions of I-SceI are the deletions I-SceI-1, I-SceI-2, I-SceI-3, I-SceI-4, I-SceI-5, I-SceI-6, I-SceI-7, I-SceI-8, I-SceI-9 or the mutants S229K and S229A, in combination with the mutation M202K.
Even more preferred are the deletions I-SceI-1, I-SceI-2, I-SceI-3, I-SceI-4, I-SceI-5, I-SceI-6 or the mutant S229K in combination with the mutation M202K.
In another embodiment of the invention, the amino acids glutamine at position 76, glutamic acid at position 129, or tyrosine at position 198 of the amino acid sequence of wildtype I-SceI as disclosed in SEQ ID No. 1 (being amino acids 77, 130 and 199 if referenced to SEQ ID No. 2), are mutated to Lys, His or Arg. Thereby creating the I-SceI mutants Q76K, Q76H, Q76R, E129K, E129H, E129R, Y198K, Y198H and Y198R.
The deletions and mutations described above will also be applicable to its homologs of I-SceI having at least 55%, 58%, 60%, 70%, 80%, 85%, 90%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% sequence identity on amino acid level and having an amino acid sequence TISSETFLK at the C-terminus.
Accordingly, in one embodiment of the invention, the optimized endonuclease, is an optimized version of I-SceI or one of its homologs having at least 55%, 58%, 60%, 70%, 80%, 85%, 90%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% sequence identity on amino acid level, and having one or more of the mutations or deletions selected from the group of: I-SceI-1, I-SceI-2, I-SceI-3, I-SceI-4, I-SceI-5, I-SceI-6, I-SceI-7, I-SceI-8, I-SceI-9, S229K, S229A, S229P, S229G, S229E, S229Q, S229D, S229N, S229C, S229Y, S229T, M202K, M202H, M202R, Q76K, Q76H, Q76R, E129K, E129H, E129R, Y198K, Y198H and Y198R, wherin the amino acid numbers are referenced to the amino acid sequence as described by SEQ ID NO: 1.
In a further embodiment of the invention, the optimized endonuclease, is an optimized version of I-SceI or one of its homologs having at least 55%, 58%, 60%, 70%, 80%, 85%, 90%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% sequence identity on amino acid level, and having one or more of the mutations or deletions selected from the group of: I-SceI-1, I-SceI-2, I-SceI-3, I-SceI-4, I-SceI-5, I-SceI-6, S229K and M202K, wherin the amino acid numbers are referenced to the amino acid sequence as described by SEQ ID NO: 1.
A particular preferred optimized endonuclease is a wildtype or engineered version of I-SceI, as described by SEQ ID NO: 1 or one of its homologs having at least 55%, 58%, 60%, 70%, 80%, 85%, 90%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% sequence identity on amino acid level and having one or more mutations selected from the groups of:
a) I-SceI-1, I-SceI-2, I-SceI-3, I-SceI-4, I-SceI-5, I-SceI-6, I-SceI-7, I-SceI-8 and I-SceI-9;
b) S229K, S229A, S229P, 5229G, S229E, S229Q, S229D, S229N, S229C, S229Y, S229T, M203K, M203H, M203R, Q77K, Q77H, Q77R, E130K, E130H, E130R, Y199K, Y199H and Y199R;
c) a methionine, valine, glycine, threoninr, serine, alanine, cysteine, glutamic acid, glutamine, aspartic acid, asparagine, isoleucine or histidine after the start methionine of their amino acid sequence; or
d) a combination of one or more mutations selected from a) and b), a) and c), b) and c) or a) b) and c) above.
The optimized endonuclease is preferably expressed as a fusion protein with a nuclear localization sequence (NLS). This NLS sequence enables facilitated transport into the nucleus and increases the efficacy of the recombination system. A variety of NLS sequences are known to the skilled worker and described, inter alia, by Jicks G R and Raikhel N V (1995) Annu. Rev. Cell Biol. 11:155-188. Preferred for plant organisms is, for example, the NLS sequence of the SV40 large antigen. Examples are provided in WO 03/060133. The NLS may be heterologous to the endonuclease and/or the DNA binding domain or may be naturally comprised within the endonuclease and/or DNA binding domain.
Another embodiment of the invention are translational fusions comprising optimized endonucleases and heterologous DNA binding domains. The optimized endonucleases comprise mutations as described above and may or may not comprise additional mutations as described above e.g. mutations used to create engineered endonucleases.
Preferred heterologous DNA binding domains are zinc finger or repeat units derived from a transcription activator-like (TAL) effector (also called TAL repeat).
Accordingly, in one embodiment of the invention, the optimized endonuclease is fused to at least one zinc finger domain, or a at least one repeat units derived from a transcription activator-like (TAL) effector, or at least one zinc finger domain and at least one repeat units derived from a transcription activator-like (TAL) effector.
Those fusions might be N-terminal or C-terminal or N- and C-terminal to the optimized endonulease.
For example, it is possible to fuse at least one at least one zinc finger domain to the N-Terminus and at least one zinc finger domain to the C-terminus of the optimized endonuclease, or to fuse at least one zinc finger domain to the N-terminus and at least one repeat unit derived from a transcription activator-like (TAL) effector to the C-terminus of the optimized endonuclease. Alternatively, it is also possible to fuse a combination of at least one zinc-finger domain and at least one repeat unit derived from a transcription activator-like (TAL) effector to the N- or C-terminus or to the N- and C-terminus of an optimized endonuclease. Basically every permutation of those elements is possible.
Zinc finger domains have conserved cysteine and histidine residues that tetrahedycally-coordinate the single zinc atom in each finger domain. In particular, most ZFPs are characterized by finger components of the general sequence:

-Cys-(X)2-4-Cys-(X)12-His-(X)3-5-His- (SEQ ID NO: 42),

in which X represents any amino acid (the C2H2 ZFPs). The zinc-finger domains of this most widely represented class contains two cysteines and two histidines with particular spacings. The folded structure of each finger domain contains an antiparallel beta-turn, a finger tip region and a short amphipathic alpha-10 helix. The metal coordinating ligands bind to the zinc ion and, in the case of zif268-type zinc fingers, the short amphipathic a-helix binds in the major groove ofDNA. In addition, the structure of the zinc finger is stabilized by certain conserved hydrophobic amino acid residues (e.g., the residue directly preceding the first conserved Cys and the residue at position +4 of the helical segment of the finger) and by zinc coordination 15 through the conserved cysteine and histidine residues. Canonical C2H2 ZFPs having alterations in positions making direct base contacts, ‘supporting’ or ‘buttressing’ residues immediately adjacent to the base-contacting positions, and positions capable of contacting the phosphate backbone ofthe DNA have been described. See, e.g., U.S. Pat. Nos. 6,007,988; 6,013,453; 6,140,081; 6,866,997; 6,746,838; 6,140,081; 6,610,512; 7,101,972; 6,453,242; 6,785,613; 7,013,219; PCT WO 98/53059; Choo et aI. (2000) Curro Opin. Struct. Biol. 10:411-416; Segal et aI. (2000) Curro Opin. Chern. Biol. 4:34-39.
In addition, zinc finger proteins containing zinc fingers with modified zinc coordinating residues have also been described (see, e.g., U.S. patent application Ser. Nos. 25 20030108880, 20060246567 and 20060246588; the disclosures ofwhich are incorporated by reference).
The terms “repeat unit derived from a transcription activator-like (TAL) effector”, “repeat unit” and “TAL repeat” are used exchangebly and are used to describe the modular portion of a repeat domain from a TAL effector, or an artificial version thereof, that contains two amino acids in positions 12 and 13 of the amino acid sequence of a repeat unit that determine recognition of a base pair in a target DNA sequence that such amino acids confer recognition of, as follows: HD for recognition of C/G; NI for recognition of NT; NG for recognition of T/A; NS for recognition of C/G or NT or T/A or G/C; NN for recognition of G/C or A/T; IG for recognition of T/A; N for recognition of C/G; HG for recognition of C/G or T/A; H for recognition of T/A; and NK for recognition of G/C.
(the amino acids H, D, I, G, S, K are described in one-letter code, whereby A, T, C, G refer to the DNA base pairs recognized by the amino acids)
The number of repeat units to be used in a repeat domain can be ascertained by one skilled in the art by routine experimentation. Generally, at least 1.5 repeat units are considered as a minimum, although typically at least about 8 repeat units will be used. The repeat units do not have to be complete repeat units, as repeat units of half the size can be used. A heterologous DNA binding domain of the invention can comprise, for example, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 5.5, 6, 6.5, 7, 7.5, 8, 8.5, 9, 9.5, 10, 10.5, 11, 11.5, 12, 12.5, 13, 13.5, 14, 14.5, 15, 15.5, 16, 16.5, 17, 17.5, 18, 18.5, 19, 19.5, 20, 20.5, 21, 21.5, 22, 22.5, 23, 23.5, 24, 24.5, 25, 25.5, 26, 26.5, 27, 27.5, 28, 28.5, 29, 29.5, 30, 30.5, 31, 31.5, 32, 32.5, 33, 33.5, 34, 34.5, 35, 35.5, 36, 36.5, 37, 37.5, 38, 38.5, 39, 39.5, 40, 40.5, 41, 41.5, 42, 42.5, 43, 43.5, 44, 44.5, 46, 46.5, 47, 47.5, 48, 48.5, 49, 49.5, 50, 50.5 or more repeat units.
A typical consensus sequence of a repeat with 34 amino acids (in one-letter code) is shown below:









(SEQ ID NO: 19)



LTPEQVVAIASNGGGKQALETVQRLLPVLCQAHG






A further consensus sequence for a repeat unit with 35 amino acids (in one-letter code) is as follows:









(SEQ ID NO: 20)



LTPEQVVAIASNGGGKQALETVQRLLPVLCQAPHD






The repeat units which can be used in one embodiment of the invention have an identity with the consensus sequences described above of at least 35%, 40%, 50%, 60%, 70%, 75%, 80%, 85%, 90% or 95%.
Zinc finger domains as well as TAL repeats can be mutated to bind to any given polynucleotide sequence. Methods how to select appropriate mutations are disclosed in WO0027878, WO03062455, WO08076290, WO08076290, WO9945132 and WO2010/079430 included herein by reference.
It is therefore possible to select a polynucleotide sequence close to a DNA recognition sequence of an optimized endonuclease, and to mutate zinc finger domains or TAL repeats to bind those neighbouring polynucleotide sequence. Those zinc finger domains or TAL repeats can then be used for translational fusions with the respective optimized endonuclease, having the DNA recognition sequence close by.
It is also possible to choose a polynucleotide sequence similar to a DNA recognition sequence of an optimized endonuclease but being inefficiently recognized and or cut by the optimized endonuclease. It is possible to create translational fusions of optimized endonucleases with at least one zinc finger or TAL repeat, binding to a polynucleotide sequence close to this non-optimal DNA recognition site, which will recognize and cut said non-optimal DNA recognition site more efficiently.
It is possible to generate fusions of optimized LAGLIDADG nucleases with a combination of TAL repeat and Zinc finger domains. As TAL effectors are able to recognize AT rich regions, this might compensate the limitation of Zinc finger domains, which preferably bind to GC rich regions.
TAL repeat and Zinc finger domains domains can be used to create N-terminal or C-terminal or N-terminal and C-terminal fusions to optimized LAGLIDADG nucleases, wherein several TAL repeats and or Zinc finger domains as well as combinations of these can be fused at the N-terminal or C-terminal end of the optimized LAGLIDADG nucleases.
Exemplary structures of such fusions are:
N-term-I-SceI-TAL repeat (x)-C-term
N-term-TAL repeat(x) I-SceI- -C-term
N-term-TAL repeat(x) I-SceI-TAL repeat-C-term
N-term-I-SceI-Zinc finger domain (x)-C-term
N-term-Zinc finger domain(x) I-SceI- -C-term
N-term-Zinc finger domain(x) I-SceI-Zinc finger domain(x)-C-term
N-term-TAL repeat(x)-I-SceI-Zinc finger domain(x)-C-term
N-term-Zinc finger domain(x) I-SceI-TAL repeat-C-term
N-term-TAL repeat(x)-I-SceI-Zinc finger domain(x)-C-term
N-term-Zinc finger domain(x) I-SceI-TAL repeat-C-term
N-term-Zinc finger domain(x)-TAL repeat(x)-I-SceI-Zinc finger domain(x)-C-term
N-term-Zinc finger domain(x) I-SceI-TAL repeat(x)-Zinc finger domain(x)-C-term,
wherein (x) means one or several TAL repeats or Zinc finger domains.
In a preferred embodiment, the sequences encoding the optimized endonucleases are modified by insertion of an intron sequence. This prevents expression of a functional enzyme in procaryotic host organisms and thereby facilitates cloning and transformations procedures (e.g., based on E. coli or Agrobacterium). In eukaryotic organisms, for example plant organisms, expression of a functional enzyme is realized, since plants are able to recognize and “splice” out introns. Preferably, introns are inserted in the optimized endonucleases mentioned as preferred above.
In another preferred embodiment, the amino acid sequences of the optimized endonuclease can be modified by adding a Sec IV secretion signal to the N-, or C-Terminus of the optimized endonuclease.
In a preferred embodiment the SecIV secretion signal is a SecIV secretion signal comprised in Vir proteins of Agrobacterium. Examples of such Sec IV secretion signals as well as methods how to apply these are disclosed in WO 01/89283, in Vergunst et al, Positive charge is an important feature of the C-terminal transport signal of the VirB/D4-translocated proteins of Agrobacterium, PNAS 2005, 102, 03, pages 832 to 837.
A Sec IV secretion signal might also be added, by adding fragments of a Vir protein or even a complete Vir protein, for example a complete VirE2 protein to an optimized endonuclease, in a similar way as described in the description of WO01/38504, which describes a RecA/VirE2 fusion protein.
In another preferred embodiment the amino acid sequences of the optimized endonuclease can be modified by adding a Sec III secretion signal to the N-, or C-Terminus of the optimized endonuclease. Suitable SecIII secretion signals are for example disclosed in WO 00/02996.
In case a Sec III secretion signal is added, it can be of advantage, to express the optimized endonuclease in a cell, which does also comprise a recombinant construct encoding parts of or a complete functional type III secretion system, in order to overexpress or complement parts or the complete functional type III secretion system in such cell.
Recombinant constructs encoding parts or a complete functional type III secretion system are for example disclosed in WO 00/02996.
If a SecIV secretion signal is added to the optimized endonuclease and the optimized endonuclease is intended to be expressed for example in Agrobacterium rhizogenes or in Agrobacterium tumefaciens, it is of advantage to adapt the DNA sequence coding for the optimized endonuclease to the codon usage of the expressing organism. Preferably the optimized endonuclease does not have or has only few DNA recognition sequences in the genome of the expressing organism. It is of even greater advantage, if the optimized endonuclease does not have a DNA recognition sequence or less preferred DNA recognition sequence in the Agrobacterium genome. In case the optimized endonuclease is intended to be expressed in a prokaryotic organism the optimized endonuclease encoding sequence must not have an intron.
Polynucleotides:
The invention does also comprise isolated polynucleotides coding for the optimized endonucleases described above.
Examples of such isolated polynucleotides are isolated polynucleotides coding for amino acid sequences described by SEQ ID NO: 3, 5, or amino acid sequences having at least 70%, 80%, 90% 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% amino acid sequence similarity, preferably having at least 70%, 80%, 90% 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% amino acid sequence identity to any one of the amino acid sequences described by SEQ ID NO:2, 3, 5.
Preferably the isolated polynucleotide has a optimized codon usage for expression in a particular host organism, or has a low content of RNA instability motifs, or has a low content of codon repeats, or has a low contend of cryptic splice sites, or has a low content of alternative start codons, or has a low content of restriction sites, or has a low content of RNA secondary structures or has any combination of these features.
The codon usage of the isolated polypeptide may be optimized e.g. for the expression in plants, preferably in a plant selected from the group comprising: rice, corn, wheat, rape seed, sugar cane, sunflower, sugar beet, potato or tobacco.
Preferably the isolated polynucleotide is combined with a promoter sequence and a terminator sequence suitable to form a functional expression cassette for expression of the optimized endonuclease in a particular host organism.
Suitable promoters are for example constitutive, heat- or pathogen-inducible, or seed, pollen, flower or fruit specific promoters.
The person skilled in the art knows numerous promoters having those features.
For example several constitutive promoters in plants are known. Most of them are derived from viral or bacterial sources such as the nopaline synthase (nos) promoter (Shaw et al. (1984) Nucleic Acids Res. 12 (20):7831-7846), the mannopine synthase (mas) promoter (Co-mai et al. (1990) Plant Mol Biol 15(3):373-381), or the octopine synthase (ocs) pro-moter (Leisner and Gelvin (1988) Proc Natl Acad Sci USA 85 (5):2553-2557) from Agrobacterium tumefaciens or the CaMV35S promote from the Cauliflower Mosaic Vi-rus (U.S. Pat. No. 5,352,605). The latter was most frequently used in constitutive expression of transgenes in plants (Odell et al. (1985) Nature 313:810-812; Battraw and Hall (1990) Plant Mol Biol 15:527-538; Benfey et al. (1990) EMBO J 9(69):1677-1684; U.S. Pat. No. 5,612,472). However, the CaMV 35S promoter demonstrates variability not only in dif-ferent plant species but also in different plant tissues (Atanassova et al. (1998) Plant Mol Biol 37:275-85; Battraw and Hall (1990) Plant Mol Biol 15:527-538; Holtorf et al. (1995) Plant Mol Biol 29:637-646 ; Jefferson et al. (1987) EMBO J 6:3901-3907). An additional disadvantage is an interference of the transcription regulating activity of the 35S promoter with wild-type CaMV virus (Al-Kaff et al. (2000) Nature Biotechnology 18 :995-99). Another viral promoter for constitutive expression is the Sugarcane bacilliform badnavirus (ScBV) promoter (Schenk et al. (1999) Plant Mol Biol 39 (6) :1221-1230).
Several plant constitutive promoters are described such as the ubiquitin promoter from Arabidopsis thaliana (Callis et al. (1990) J Biol Chem 265:12486-12493; Holtorf S et al. (1995) Plant Mol Biol 29:637-747), which—however—is reported to be unable to regu-late expression of selection markers (WO03102198), or two maize ubiquitin promoter (Ubi-1 and Ubi-2; U.S. Pat. Nos. 5,510,474; 6,020,190; 6,054,574), which beside a consti-tutive expression profile demonstrate a heat-shock induction (Christensen et al. (1992) Plant. Mol. Biol. 18(4):675-689). A comparison of specificity and expression level of the CaMV 35S, the barley thionine promoter, and the Arabidopsis ubiquitin promoter based on stably transformed Arabidopsis plants demonstrates a high expression rate for the CaMV 35S promoter, while the thionine promoter was inactive in most lines and the ubil promoter from Arabisopsis resulted only in moderate expression activity (Holtorf et al. (1995) Plant Mol Biol 29 (4):637-6469).
Vectors:
The polynucleotides described above may be comprised in a DNA vector suitable for transformation, transfection, cloning or overexpression.
In one example, the polynucleotides described above are comprised in a vector for transformation of non-human organisms or cells, preferably the non-human organisms are plants or plant cells.
The vectors of the invention usually comprise further functional elements, which may include but shall not be limited to:
i) Origins of replication which ensure replication of the expression cassettes or vectors according to the invention in, for example, E. coli. Examples which may be mentioned are ORI (origin of DNA replication), the pBR322 on or the P15A ori (Sam-brook et al.: Molecular Cloning. A Laboratory Manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989).
ii) Multiple cloning sites (MCS) to enable and facilitate the insertion of one or more nucleic acid sequences.
iii) Sequences which make possible homologous recombination or insertion into the genome of a host organism.
iv) Elements, for example border sequences, which make possible the Agrobacterium-mediated transfer in plant cells for the transfer and integration into the plant genome, such as, for example, the right or left border of the T-DNA or the vir region.
The Marker Sequence
The term “marker sequence” is to be understood in the broad sense to include all nucleotide sequences (and/or polypeptide sequences translated therefrom) which facilitate detection, identification, or selection of transformed cells, tissues or organism (e.g., plants). The terms “sequence allowing selection of a transformed plant material”, “selection marker” or “selection marker gene” or “selection marker protein” or “marker” have essentially the same meaning.
Markers may include (but are not limited to) selectable marker and screenable marker. A selectable marker confers to the cell or organism a phenotype resulting in a growth or viability difference. The selectable marker may interact with a selection agent (such as a herbicide or anti-biotic or pro-drug) to bring about this phenotype. A screenable marker confers to the cell or organism a readily detectable phenotype, preferably a visibly detectable phenotype such a color or staining. The screenable marker may interact with a screening agent (such as a dye) to bring about this phenotype.
Selectable marker (or selectable marker sequences) comprise but are not limited to
a) negative selection marker, which confers resistance against one or more toxic (in case of plants phytotoxic) agents such as an antibiotica, herbicides or other biocides,
b) counter selection marker, which confer a sensitivity against certain chemical compounds (e.g., by converting a non-toxic compound into a toxic compound), and
c) positive selection marker, which confer a growth advantage (e.g., by expression of key elements of the cytokinin or hormone biosynthesis leading to the production of a plant hormone e.g., auxins, gibberllins, cytokinins, abscisic acid and ethylene; Ebi-numa H et al. (2000) Proc Natl Acad Sci USA 94:2117-2121).
When using negative selection markers, only cells or plants are selected which comprise said negative selection marker. When using counter selection marker, only cells or plants are selected which lack said counter-selection marker. Counter-selection marker may be employed to verify successful excision of a sequence (comprising said counter-selection marker) from a genome. Screenable marker sequences include but are not limited to reporter genes (e. g. luciferase, glucuronidase, chloramphenicol acetyl transferase (CAT, etc.). Preferred marker sequences include but shall not be limited to:
i) Negative Selection Marker
As a rule, negative selection markers are useful for selecting cells which have success-fully undergone transformation. The negative selection marker, which has been introduced with the DNA construct of the invention, may confer resistance to a biocide or phytotoxic agent (for example a herbicide such as phosphinothricin, glyphosate or bromoxynil), a metabolism inhibitor such as 2-deoxyglucose-6-phosphate (WO 98/45456) or an antibiotic such as, for example, tetracyclin, ampicillin, kanamycin, G 418, neomycin, bleomycin or hygromycin to the cells which have successfully under-gone transformation. The negative selection marker permits the selection of the trans-formed cells from untransformed cells (McCormick et al. (1986) Plant Cell Reports 5:81-84). Negative selection marker in a vector of the invention may be employed to confer resistance in more than one organism. For example a vector of the invention may comprise a selection marker for amplification in bacteria (such as E. coli or Agrobacterium) and plants. Examples of selectable markers for E. coli include: genes specifying resistance to antibiotics, i.e., ampicillin, tetracycline, kanamycin, erythromycin, or genes conferring other types of selectable enzymatic activities such as galactosidase, or the lactose operon. Suitable selectable markers for use in mammalian cells include, for example, the dihydrofolate reductase gene (DHFR), the thymidine kinase gene (TK), or prokaryotic genes conferring drug resistance, gpt (xanthine-guanine phosphoribosyltransferase, which can be selected for with mycophenolic acid; neo (neomycin phosphotransferase), which can be selected for with G418, hygromycin, or puromycin; and DHFR (dihydrofolate reductase), which can be selected for with methotrexate (Mulligan & Berg (1981) Proc Natl Acad Sci USA 78:2072; Southern & Berg (1982) J Mol Appl Genet 1: 327). Selection markers for plant cells often confer resistance to a biocide or an antibiotic, such as, for example, kanamycin, G 418, bleomycin, hygromycin, or chloramphenicol, or herbicide resistance, such as resistance to chlorsulfuron or Basta.
Especially preferred negative selection markers are those which confer resistance to herbicides. Examples of negative selection markers are:

    
    
        DNA sequences which encode phosphinothricin acetyltransferases (PAT), which acetylates the free amino group of the glutamine synthase inhibitor phosphinothricin (PPT) and thus brings about detoxification of PPT (de Block et al. (1987) EMBO J 6:2513-2518) (also referred to as Bialophos—resistence gene bar; EP 242236),
        5-enolpyruvylshikimate-3-phosphate synthase genes (EPSP synthase genes), which confer resistence to Glyphosate-(N-(phosphonomethyl)glycine),
        the gox gene, which encodes the Glyphosate-degrading enzyme Glyphosate oxi-doreductase,
        the deh gene (encoding a dehalogenase which inactivates Dalapon-),
        acetolactate synthases which confer resistance to sulfonylurea and imidazolinone,
        bxn genes which encode Bromoxynil-degrading nitrilase enzymes,
        the kanamycin, or G418, resistence gene (NPTII). The NPTII gene encodes a neomycin phosphotransferase which reduces the inhibitory effect of kanamycin, neomycin, G418 and paromomycin owing to a phosphorylation reaction (Beck et al (1982) Gene 19: 327),
        the DOGR1 gene. The DOGR1 gene has been isolated from the yeast Saccharomyces cerevisiae (EP 0 807 836). It encodes a 2-deoxyglucose-6-phosphate phos-phatase which confers resistence to 2-DOG (Randez-Gil et al. (1995) Yeast 11:1233-1240).
        the hyg gene, which codes for the enzyme hygromycin phosphotransferase and confers resistance to the antibiotic hygromycin (Gritz and Davies (1983) Gene 25: 179);
        especially preferred are negative selection markers that confer resistance against the toxic effects imposed by D-amino acids like e.g., D-alanine and D-serine (WO 03/060133; Erikson 2004). Especially preferred as negative selection marker in this contest are the daol gene (EC: 1.4.3.3: GenBank Acc.-No.: U60066) from the yeast Rhodotorula gracilis (Rhodosporidium toruloides) and the E. coli gene dsdA (D-serine dehydratase (D-serine deaminase) (EC: 4.3.1.18; GenBank Acc.-No.: J01603).
    
    


ii) Positive Selection Marker
Positive selection marker comprise but are not limited to growth stimulating selection marker genes like isopentenyltransferase from Agrobacterium tumefaciens (strain: P022; Genbank Acc.-No.: AB025109) may—as a key enzyme of the cytokinin biosynthesis—facilitate regeneration of transformed plants (e.g., by selection on cyto-kinin-free medium). Corresponding selection methods are described (Ebinuma H et al. (2000) Proc Natl Acad Sci USA 94:2117-2121; Ebinuma H et al. (2000) Selection of Marker-free transgenic plants using the oncogenes (ipt, rol A, B, C) of Agrobacterium as selectable markers, In Molecular Biology of Woody Plants. Kluwer Academic Publishers). Additional positive selection markers, which confer a growth advantage to a transformed plant in comparison with a non-transformed one, are described e.g., in EP-A 0 601 092. Growth stimulation selection markers may include (but shall not be limited to) beta-Glucuronidase (in combination with e.g., a cytokinin glucuronide), mannose-6-phosphate isomerase (in combination with mannose), UDP-galactose-4-epimerase (in combination with e.g., galactose), wherein mannose-6-phosphate isomerase in combination with mannose is especially preferred.
iii) Counter Selection Markers
Counter-selection marker enable the selection of organisms with successfully deleted sequences (Koprek T et al. (1999) Plant J 19(6):719-726). TK thymidine kinase (TK) and diphtheria toxin A fragment (DT-A), codA gene encoding a cytosine deaminase (Gleve A P et al. (1999) Plant Mol Biol 40(2):223-35; Pereat R I et al. (1993) Plant Mol Biol 23(4):793-799; Stougaard J (1993) Plant J 3:755-761), the cytochrome P450 gene (Koprek et al. (1999) Plant J 16:719-726), genes encoding a haloalkane dehalogenase (Naested H (1999) Plant J 18:571-576), the iaaH gene (Sundaresan Vet al. (1995) Genes & Development 9:1797-1810), the tms2 gene (Fedoroff N V & Smith D L (1993) Plant J 3:273-289), and D-amino acid oxidases causing toxic effects by conversion of D-amino acids (WO 03/060133).
In a preferred embodiment the excision cassette includes at least one of said counter-selection markers to distinguish plant cells or plants with successfully excised sequences from plant which still contain these. In a more preferred embodiment the excision cassette of the invention comprises a dual-function marker i.e. a marker with can be employed as both a negative and a counter selection marker depending on the substrate employed in the selection scheme. An example for a dual-function marker is the daol gene (EC: 1.4.3.3: GenBank Acc.-No.: U60066) from the yeast Rhodotorula gracilis, which can be employed as negative selection marker with D.-amino acids such as D-alanine and D-serine, and as counter-selection marker with D-amino acids such as D-isoleucine and D-valine (see European Patent Appl. No.: 04006358.8)
iv) Screenable Marker (Reporter Genes)
Screenable marker (such as reporter genes) encode readily quantifiable or detectable proteins and which, via intrinsic color or enzyme activity, ensure the assessment of the transformation efficacy or of the location or timing of expression. Especially preferred are genes encoding reporter proteins (see also Schenborn E, Groskreutz D. (1999) Mol Biotechnol 13(1):29-44) such as

    
    
        “green fluorescence protein” (GFP) (Chuff W L et al. (1996) Curr Biol 6:325-330; Lef-fel S M et al. (1997) Biotechniques 23(5):912-8; Sheen et al. (1995) Plant J 8(5):777-784; Haseloff et al. (1997) Proc Natl Acad Sci USA 94(6):2122-2127; Reichel et al. (1996) Proc Natl Acad Sci USA 93(12):5888-5893; Tian et al. (1997) Plant Cell Rep 16:267-271; WO 97/41228).
        Chloramphenicol transferase,
        luciferase (Millar et al. (1992) Plant Mol Biol Rep 10:324-414; Ow et al. (1986) Science 234:856-859) permits selection by detection of bioluminescence,
        beta-galactosidase, encodes an enzyme for which a variety of chromogenic substrates are available,
        beta-glucuronidase (GUS) (Jefferson et al. (1987) EMBO J 6:3901-3907) or the uidA gene, which encodes an enzyme for a variety of chromogenic substrates,
        R locus gene product: protein which regulates the production of anthocyanin pig-ments (red coloration) in plant tissue and thus makes possible the direct analysis of the promoter activity without the addition of additional adjuvants or chromogenic substrates (Dellaporta et al. (1988) In: Chromosome Structure and Function: Impact of New Concepts, 18th Stadler Genetics Symposium, 11:263-282,),
        beta-lactamase (Sutcliffe (1978) Proc Natl Acad Sci USA 75:3737-3741), enzyme for a variety of chromogenic substrates (for example PADAC, a chromogenic cepha-losporin),
        xylE gene product (Zukowsky et al. (1983) Proc Natl Acad Sci USA 80:1101-1105), catechol dioxygenase capable of converting chromogenic catechols,
        alpha-amylase (Ikuta et al. (1990) Bio/technol. 8:241-242),
        tyrosinase (Katz et al. (1983) J Gene Microbiol 129:2703-2714), enzyme which oxi-dizes tyrosine to give DOPA and dopaquinone which subsequently form melanine, which is readily detectable,
        aequorin (Prasher et al. (1985) Biochem Biophys Res Commun 126(3):1259-1268), can be used in the calcium-sensitive bioluminescence detection.
    
    


Target Organisms
Any organism suitable for transformation or delivery of an optimized endonuclease can be used as target organism. This includes prokaryotes, eukaryotes, and archaea, in particular human or animal cells, animals, plants, fungi or yeasts, preferably plants, fungi or yeasts.
In one embodiment the target organism is a plant.
The term “plant” includes whole plants, shoot vegetative organs/structures (e. g. leaves, stems and tubers), roots, flowers and floral organs/structures (e. g. bracts, sepals, petals, stamens, carpels, anthers and ovules), seeds (including embryo, endosperm, and seed coat) and fruits (the mature ovary), plant tissues (e. g. vascular tissue, ground tissue, and the like) and cells (e. g. guard cells, egg cells, trichomes and the like), and progeny of same. The class of plants that can be used in the method of the invention is generally as broad as the class of higher and lower plants amenable to transformation techniques, including angiosperms (monocotyledonous and dicotyledonous plants), gymnosperms, ferns, and multicellular algae. It includes plants of a variety of ploidy levels, including aneuploid, polyploid, diploid, haploid and hemizygous.
Included within the scope of the invention are all genera and species of higher and lower plants of the plant kingdom. Included are furthermore the mature plants, seed, shoots and seedlings, and parts, propagation material (for example seeds and fruit) and cultures, for example cell cultures, derived therefrom.
Preferred are plants and plant materials of the following plant families: Amaranthaceae, Brassicaceae, Carophyllaceae, Chenopodiaceae, Compositae, Cucurbitaceae, Labi-atae, Leguminosae, Papilionoideae, Liliaceae, Linaceae, Malvaceae, Rosaceae, Saxi-fragaceae, Scrophulariaceae, Solanaceae, Tetragoniaceae.
Annual, perennial, monocotyledonous and dicotyledonous plants are preferred host organisms for the generation of transgenic plants. The use of the recombination system, or method according to the invention is furthermore advantageous in all ornamental plants, useful or ornamental trees, flowers, cut flowers, shrubs or turf. Said plant may include—but shall not be limited to—bryophytes such as, for example, Hepaticae (hepaticas) and Musci (mosses); pteridophytes such as ferns, horsetail and club-mosses; gymnosperms such as conifers, cycads, ginkgo and Gnetaeae; algae such as Chlorophyceae, Phaeophpyceae, Rhodophyceae, Myxophyceae, Xanthophyceae, Bacillariophyceae (diatoms) and Euglenophyceae.
Plants for the purposes of the invention may comprise the families of the Rosaceae such as rose, Ericaceae such as rhododendrons and azaleas, Euphorbiaceae such as poinsettias and croton, Caryophyllaceae such as pinks, Solanaceae such as petunias, Gesneriaceae such as African violet, Balsaminaceae such as touch-me-not, Orchida-ceae such as orchids, Iridaceae such as gladioli, iris, freesia and crocus, Compositae such as marigold, Geraniaceae such as geraniums, Liliaceae such as drachaena, Moraceae such as ficus, Araceae such as philodendron and many others.
The transgenic plants according to the invention are furthermore selected in particular from among dicotyledonous crop plants such as, for example, from the families of the Leguminosae such as pea, alfalfa and soybean; Solanaceae such as tobacco and and many others; the family of the Umbelliferae, particularly the genus Daucus (very particularly the species carota (carrot)) and Apium (very particularly the species graveolens dulce (celery)) and many others; the family of the Solanaceae, particularly the genus Lycopersicon, very particularly the species esculentum (tomato) and the genus Solanum, very particularly the species tuberosum (potato) and melongena (au-bergine) and many others; and the genus Capsicum, very particularly the species an-num (pepper) and many others; the family of the Leguminosae, particularly the genus Glycine, very particularly the species max (soybean) and many others; and the family of the Cruciferae, particularly the genus Brassica, very particularly the species napus (oilseed rape), campestris (beet), oleracea cv Tastie (cabbage), oleracea cv Snowball Y (cauliflower) and oleracea cv Emperor (broccoli); and the genus Arabidopsis, very particularly the species thaliana and many others; the family of the Compositae, par-ticularly the genus Lactuca, very particularly the species sativa (lettuce) and many others.
The transgenic plants according to the invention are selected in particular among monocotyledonous crop plants, such as, for example, cereals such as wheat, barley, sorghum and millet, rye, triticale, maize, rice or oats, and sugar cane. Especially preferred are Arabidopsis thaliana, Nicotiana tabacum, oilseed rape, soybean, corn (maize), wheat, linseed, potato and tagetes.
Plant organisms are furthermore, for the purposes of the invention, other organisms which are capable of photosynthetic activity, such as, for example, algae or cyanobacteria, and also mosses. Preferred algae are green algae, such as, for example, algae of the genus Haematococcus, Phaedactylum tricornatum, Volvox or Dunaliella. 
Genetically modified plants according to the invention which can be consumed by humans or animals can also be used as food or feedstuffs, for example directly or following processing known in the art.
Construction of Polynucleotide Constructs
Typically, polynucleotide constructs (e.g., for an expression cassette) to be introduced into non-human organism or cells, e.g. plants or plant cells are prepared using transgene expression techniques. Recombinant expression techniques involve the construction of recombinant nucleic acids and the expression of genes in transfected cells. Molecular cloning techniques to achieve these ends are known in the art. A wide variety of cloning and in vitro amplification methods suitable for the construction of recombinant nucleic acids are well-known to persons of skill in the art. Examples of these techniques and instructions sufficient to direct persons of skill in the art through many cloning exercises are found in Berger and Kimmel, Guide to Molecular Cloning Techniques, Methods in Enzymology, Vol. 152, Academic Press, hic., San Diego, Calif. (Berger); Current Protocols in Molecular Biology, F. M. Ausubel et al., eds., Current Protocols, a joint venture between Greene Publish-ing Associates, Inc. and John Wiley & Sons, Inc., (1998 Supplement), T. Maniatis, E. F. Fritsch and J. Sambrook, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. (1989), in T. J. Silhavy, M. L. Berman and L. W. Enquist, Experiments with Gene Fusions, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. (1984). Preferably, the DNA constructs employed in the invention are generated by joining the abovementioned essential constituents of the DNA construct together in the abovementioned sequence using the recombination and cloning techniques with which the skilled worker is familiar.
The construction of polynucleotide constructs generally requires the use of vectors able to replicate in bacteria. A plethora of kits are commercially available for the purification of plasmids from bacteria. The isolated and purified plasmids can then be further manipulated to produce other plasmids, used to transfect cells or incorporated into Agrobacterium tumefaciens or Agrobacterium rhizogenes to infect and transform plants. Where Agrobacterium is the means of transformation, shuttle vectors are constructed.
Methods for Introducing Constructs into Target Cells
A DNA construct employed in the invention may advantageously be introduced into cells using vectors into which said DNA construct is inserted. Examples of vectors may be plasmids, cosmids, phages, viruses, retroviruses or agrobacteria. In an advantageous embodiment, the expression cassette is introduced by means of plasmid vectors. Preferred vectors are those which enable the stable integration of the expression cassette into the host genome.
A DNA construct can be introduced into the target plant cells and/or organisms by any of the several means known to those of skill in the art, a procedure which is termed transformation (see also Keown et al. (1990) Meth Enzymol 185:527-537). For instance, the DNA constructs can be introduced into cells, either in culture or in the organs of a plant by a variety of conventional techniques. For example, the DNA constructs can be introduced directly to plant cells using ballistic methods, such as DNA particle bombardment, or the DNA construct can be introduced using techniques such as electroporation and microinjection of cells. Particle-mediated transformation techniques (also known as “biolistics”) are described in, e.g., Klein et al. (1987) Nature 327:70-73; Vasil Vet al. (1993) BiolTechnol 11:1553-1558; and Becker D et al. (1994) Plant J 5:299-307. These methods involve penetration of cells by small particles with the nucleic acid either within the matrix of small beads or particles, or on the surface. The biolistic PDS-1000 Gene Gun (Biorad, Hercules, Calif.) uses helium pressure to accelerate DNA-coated gold or tungsten microcarriers toward target cells. The process is applicable to a wide range of tissues and cells from organisms, including plants. Other transformation methods are also known to those of skill in the art.
Microinjection techniques are known in the art and are well described in the scientific and patent literature. Also, the cell can be permeabilized chemically, for example using polyethylene glycol, so that the DNA can enter the cell by diffusion. The DNA can also be introduced by protoplast fusion with other DNA-containing units such as minicells, cells, lysosomes or liposomes. The introduction of DNA constructs using polyethylene glycol (PEG) precipitation is described in Paszkowski et al. (1984) EMBO J 3:2717. Liposome-based gene delivery is e.g., described in WO 93/24640; Mannino and Gould-Fogerite (1988) BioTechniques 6(7):682-691; U.S. Pat. No. 5,279,833; WO 91/06309; and Feigner et al. (1987) Proc Natl Acad Sci USA 84:7413-7414).
Another suitable method of introducing DNA is electroporation, where the cells are permeabilized reversibly by an electrical pulse. Electroporation techniques are described in Fromm et al. (1985) Proc Natl Acad Sci USA 82:5824. PEG-mediated transformation and electroporation of plant protoplasts are also discussed in Lazzeri P (1995) Methods Mol Biol 49:95-106. Preferred general methods which may be mentioned are the calcium-phosphate-mediated transfection, the DEAE-dextran-mediated transfection, the cationic lipid-mediated transfection, electroporation, transduction and infection. Such methods are known to the skilled worker and described, for example, in Davis et al., Basic Methods In Molecular Biology (1986). For a review of gene transfer methods for plant and cell cultures, see, Fisk et al. (1993) Scientia Horticulturae 55:5-36 and Potrykus (1990) CIBA Found Symp 154:198.
Methods are known for introduction and expression of heterologous genes in both monocot and dicot plants. See, e.g., U.S. Pat. Nos. 5,633,446, 5,317,096, 5,689,052, 5,159,135, and 5,679,558; Weising et al. (1988) Ann. Rev. Genet. 22: 421-477. Transformation of monocots in particular can use various techniques including electroporation (e.g., Shimamoto et al. (1992) Nature 338:274-276; biolistics (e.g., EP-A1 270,356); and Agrobacterium (e.g., Bytebier et al. (1987) Proc Natl Acad Sci USA 84:5345-5349).
In plants, methods for transforming and regenerating plants from plant tissues or plant cells with which the skilled worker is familiar are exploited for transient or stable transformation. Suitable methods are especially protoplast transformation by means of poly-ethylene-glycol-induced DNA uptake, biolistic methods such as the gene gun (“particle bombardment” method), electroporation, the incubation of dry embryos in DNA-containing solution, sonication and microinjection, and the transformation of intact cells or tissues by micro- or macroinjection into tissues or embryos, tissue electroporation, or vacuum infiltration of seeds. In the case of injection or electroporation of DNA into plant cells, the plasmid used does not need to meet any particular requirement. Simple plasmids such as those of the pUC series may be used. If intact plants are to be regenerated from the transformed cells, the presence of an additional selectable marker gene on the plasmid is useful.
In addition to these “direct” transformation techniques, transformation can also be carried out by bacterial infection by means of Agrobacterium tumefaciens or Agrobacterium rhizogenes. These strains contain a plasmid (Ti or Ri plasmid). Part of this plasmid, termed T-DNA (transferred DNA), is transferred to the plant following Agrobacterium infection and integrated into the genome of the plant cell.
For Agrobacterium-mediated transformation of plants, a DNA construct of the invention may be combined with suitable T-DNA flanking regions and introduced into a conventional Agrobacterium tumefaciens host vector. The virulence functions of the A. tumefaciens host will direct the insertion of a transgene and adjacent marker gene(s) (if present) into the plant cell DNA when the cell is infected by the bacteria. Agrobacterium tumefaciens-mediated transformation techniques are well described in the scientific literature. See, for example, Horsch et al. (1984) Science 233:496-498, Fraley et al. (1983) Proc Natl Acad Sci USA 80:4803-4807, Hooykaas (1989) Plant Mol Biol 13:327-336, Horsch R B (1986) Proc Natl Acad Sci USA 83(8):2571-2575), Bevans et al. (1983) Nature 304:184-187, Bechtold et al. (1993) Comptes Rendus De L'Academie Des Sciences Serie III—Sciences De La Vie—Life Sciences 316:1194-1199, Valvekens et al. (1988) Proc Natl Acad Sci USA 85:5536-5540.
A DNA construct of the invention is preferably integrated into specific plasmids, either into a shuttle, or intermediate, vector or into a binary vector). If, for example, a Ti or Ri plasmid is to be used for the transformation, at least the right border, but in most cases the right and the left border, of the Ti or Ri plasmid T-DNA is linked with the expression cassette to be introduced as a flanking region. Binary vectors are preferably used. Bi-nary vectors are capable of replication both in E. coli and in Agrobacterium. As a rule, they contain a selection marker gene and a linker or polylinker flanked by the right or left T-DNA flanking sequence. They can be transformed directly into Agrobacterium (Holsters et al. (1978) Mol Gen Genet 163:181-187). The selection marker gene permits the selection of transformed agrobacteria and is, for example, the nptII gene, which imparts resistance to kanamycin. The Agrobacterium, which acts as host organism in this case, should already contain a plasmid with the vir region. The latter is required for transferring the T-DNA to the plant cell. An Agrobacterium thus transformed can be used for transforming plant cells.
Many strains of Agrobacterium tumefaciens are capable of transferring genetic material—for example a DNA constructs according to the invention—, such as, for example, the strains EHA101(pEHA101) (Hood E E et al. (1996) J Bacteriol 168(3):1291-1301), EHA105(pEHA105) (Hood et al. 1993, Transgenic Research 2, 208-218), LBA4404(pAL4404) (Hoekema et al. (1983) Nature 303:179-181), C58C1(pMP90) (Koncz and Schell (1986) Mol Gen Genet 204,383-396) and C58C1(pGV2260) (De-blaere et al. (1985) Nucl Acids Res. 13, 4777-4788).
The agrobacterial strain employed for the transformation comprises, in addition to its disarmed Ti plasmid, a binary plasmid with the T-DNA to be transferred, which, as a rule, comprises a gene for the selection of the transformed cells and the gene to be transferred. Both genes must be equipped with transcriptional and translational initiation and termination signals. The binary plasmid can be transferred into the agrobacterial strain for example by electroporation or other transformation methods (Mozo & Hooykaas (1991) Plant Mol Biol 16:917-918). Coculture of the plant explants with the agrobacterial strain is usually performed for two to three days.
A variety of vectors could, or can, be used. In principle, one differentiates between those vectors which can be employed for the Agrobacterium-mediated transformation or agroinfection, i.e. which comprise a DNA construct of the invention within a T-DNA, which indeed permits stable integration of the T-DNA into the plant genome. Moreover, border-sequence-free vectors may be employed, which can be transformed into the plant cells for example by particle bombardment, where they can lead both to transient and to stable expression.
The use of T-DNA for the transformation of plant cells has been studied and described intensively (EP-A1 120 516; Hoekema, In: The Binary Plant Vector System, Offset-drukkerij Kanters B. V., Alblasserdam, Chapter V; Fraley et al. (1985) Crit Rev Plant Sci 4:1-45 and An et al. (1985) EMBO J 4:277-287). Various binary vectors are known, some of which are commercially available such as, for example, pBIN19 (Clontech Laboratories, Inc. USA).
To transfer the DNA to the plant cell, plant explants are cocultured with Agrobacterium tumefaciens or Agrobacterium rhizogenes. Starting from infected plant material (for example leaf, root or stalk sections, but also protoplasts or suspensions of plant cells), intact plants can be regenerated using a suitable medium which may contain, for example, antibiotics or biocides for selecting transformed cells. The plants obtained can then be screened for the presence of the DNA introduced, in this case a DNA construct according to the invention. As soon as the DNA has integrated into the host genome, the genotype in question is, as a rule, stable and the insertion in question is also found in the subsequent generations. As a rule, the expression cassette integrated contains a selection marker which confers a resistance to a biocide (for example a herbicide) or an antibiotic such as kanamycin, G 418, bleomycin, hygromycin or phosphinotricin and the like to the transformed plant. The selection marker permits the selection of transformed cells (McCormick et al., Plant Cell Reports 5 (1986), 81-84). The plants obtained can be cultured and hybridized in the customary fashion. Two or more generations should be grown in order to ensure that the genomic integration is stable and hereditary.
The abovementioned methods are described, for example, in B. Jenes et al., Techniques for Gene Transfer, in: Transgenic Plants, Vol. 1, Engineering and Utilization, edited by S D Kung and R Wu, Academic Press (1993), 128-143 and in Potrykus (1991) Annu Rev Plant Physiol Plant Molec Biol 42:205-225). The construct to be expressed is preferably cloned into a vector which is suitable for the transformation of Agrobacterium tumefaciens, for example pBin19 (Bevan et al. (1984) Nucl Acids Res 12:8711).
The DNA construct of the invention can be used to confer desired traits on essentially any plant. One of skill will recognize that after DNA construct is stably incorporated in transgenic plants and confirmed to be operable, it can be introduced into other plants by sexual crossing. Any of a number of standard breeding techniques can be used, depending upon the species to be crossed.
The optimized endonucleases may alternatively be expressed transiently. The chimeric endonuclease may be transiently expressed as a DNA or RNA delivered into the target cell and/or may be delivered as a protein. Delivery as a protein may be achieved with the help of cell penetrating peptides or by fusion with SEcIV signal peptides fused to the nucleases or chimeric endonucleases, which mediate the secretion from a delivery organism into a cell of a target organism e.g. from Agrobacterium rhizogenes or Agrobacterium tumefaciens to a plant cell.
Regeneration of Transgenic Plants
Transformed cells, i.e. those which comprise the DNA integrated into the DNA of the host cell, can be selected from untransformed cells if a selectable marker is part of the DNA introduced. A marker can be, for example, any gene which is capable of conferring a resistance to antibiotics or herbicides (for examples see above). Transformed cells which express such a marker gene are capable of surviving in the presence of concentrations of a suitable antibiotic or herbicide which kill an untransformed wild type. As soon as a transformed plant cell has been generated, an intact plant can be obtained using methods known to the skilled worker. For example, callus cultures are used as starting material. The formation of shoot and root can be induced in this as yet undifferentiated cell biomass in the known fashion. The shoots obtained can be planted and cultured.
Transformed plant cells, derived by any of the above transformation techniques, can be cultured to regenerate a whole plant which possesses the transformed genotype and thus the desired phenotype. Such regeneration techniques rely on manipulation of certain phytohormones in a tissue culture growth medium, typically relying on a biocide and/or herbicide marker that has been introduced together with the desired nucleotide sequences. Plant regeneration from cultured protoplasts is described in Evans et al., Protoplasts Isolation and Culture, Handbook of Plant Cell Culture, pp. 124176, Macmillian Publishing Company, New York (1983); and in Binding, Regeneration of Plants, Plant Protoplasts, pp. 21-73, CRC Press, Boca Raton, (1985). Regeneration can also be obtained from plant callus, explants, somatic embryos (Dandekar et al. (1989) J Tissue Cult Meth 12:145; McGranahan et al. (1990) Plant Cell Rep 8:512), organs, or parts thereof. Such regeneration techniques are described generally in Klee et al. (1987) Ann Rev Plant Physiol 38:467-486.
Combination with Other Recombination Enhancing Techniques
In a further preferred embodiment, the efficacy of the recombination system is in-creased by combination with systems which promote homologous recombination. Such systems are described and encompass, for example, the expression of proteins such as RecA or the treatment with PARP inhibitors. It has been demonstrated that the intrachromosomal homologous recombination in tobacco plants can be increased by using PARP inhibitors (Puchta H et al. (1995) Plant J. 7:203-210). Using these inhibitors, the homologous recombination rate in the recombination cassette after induction of the sequence-specific DNA double-strand break, and thus the efficacy of the deletion of the transgene sequences, can be increased further. Various PARP inhibitors may be employed for this purpose. Preferably encompassed are inhibitors such as 3-aminobenzamide, 8-hydroxy-2-methylquinazolin-4-one (NU1025), 1,11b-dihydro-(2H) benzopyrano(4,3,2-de)isoquinolin-3-one (GPI 6150), 5-aminoisoquino-linone, 3,4-dihydro-5-(4-(1-piperidinyl)butoxy)-1(2H)-isoquinolinone, or the compounds described in WO 00/26192, WO 00/29384, WO 00/32579, WO 00/64878, WO 00/68206, WO 00/67734, WO 01/23386 and WO 01/23390.
In addition, it was possible to increase the frequency of various homologous recombination reactions in plants by expressing the E. coli RecA gene (Reiss B et al. (1996) Proc Natl Acad Sci USA 93(7):3094-3098). Also, the presence of the protein shifts the ratio between homologous and illegitimate DSB repair in favor of homologous repair (Reiss B et al. (2000) Proc Natl Acad Sci USA 97(7):3358-3363). Reference may also be made to the methods described in WO 97/08331 for increasing the homologous recombination in plants. A further increase in the efficacy of the recombination system might be achieved by the simultaneous expression of the RecA gene or other genes which increase the homologous recombination efficacy (Shalev G et al. (1999) Proc Natl Acad Sci USA 96(13):7398-402). The above-stated systems for promoting homologous recombination can also be advantageously employed in cases where the recombination construct is to be introduced in a site-directed fashion into the genome of a eukaryotic organism by means of homologous recombination.
Methods for Homologous Recombination and Targeted Mutation Using Optimized Endonucleases.
The current invention provides a method for homologous recombination of polynucleotides comprising:

    a. providing a cell competent for homologous recombination,
    b. providing a polynucleotide comprising a recombinant polynucleotide flanked by a sequence A and a sequence B,
    c. providing a polynucleotide comprising sequences A′ and B′, which are sufficiently long and homologous to sequence A and sequence B, to allow for homologous recombination in said cell and
    d. providing an optimized endonuclease or an expression cassette coding for an optimized endonuclease,
    e. combining b), c) and d) in said cell and
    f. detecting recombined polynucleotides of b) and c), or selecting for or growing cells comprising recombined polynucleotides of b) and c).


In one embodiment of the invention, step e) leads to deletion of a polynucleotide comprised in the polynucleotide provided in step c).
In one embodiment of the invention the deleted polynucleotide comprised in the polynucleotide provided in step c) codes for a marker gene or parts of a marker gene.
In one embodiment of the invention, the polynucleotide provided in step b) comprises at least one expression cassette.
In one embodiment of the invention, the polynucleotide provided in step b) comprises at least one expression cassette, leading to expression of a selection marker gene or a reporter gene.
In one embodiment of the invention, the polynucleotide provided in step b) comprises at least one expression cassette, leading to expression of a selection marker gene or a reporter gene and comprises at least one DNA recognition site or at least one chimeric recognition site.
A further embodiment of the invention provides a method for targeted mutation of polynucleotides comprising:

    a. providing a cell comprising a polynucleotide comprising an I-SceI recognition site,
    b. providing a optimized endonuclease, being able to cleave the chimeric recognition site of step a),
    c. combining a) and b) in said cell and
    d. detecting mutated polynucleotides, or selecting for growing cells comprising mutated polynucleotides.


The invention provides in another embodiment a method for homologous recombination as described above or a method for targeted mutation of polynucleotides as described above, comprising:
Combining the optimized endonuclease and the SceI recognition site via crossing of organisms, via transformation of cells or via a SecIV peptide fused to the optimized endonuclease and contacting the cell comprising the SceI recognition site with an organism expressing the optimized endonuclease and expressing a SecIV transport complex able to recognize the SecIV peptide fused to the chimeric endonuclease.
EXAMPLES
General Methods:
The chemical synthesis of oligonucleotides can be effected for example in the known manner using the phosphoamidite method (Voet, Voet, 2nd edition, Wiley Press New York, pages 896-897). The cloning steps carried out for the purposes of the present invention, such as, for example, restriction cleavages, agarose gel electrophoresis, purification of DNA fragments, the transfer of nucleic acids to nitrocellulose and nylon membranes, the linkage of DNA fragments, the transformation of E. coli cells, bacterial cultures, the propagation of phages and the sequence analysis of recombinant DNA are carried out as described by Sambrook et al. (1989) Cold Spring Harbor Laboratory Press; ISBN 0-87969-309-6. Recombinant DNA molecules were sequenced using an ALF Express laser fluorescence DNA sequencer (Pharmacia, Upsala [sic], Sweden) following the method of Sanger (Sanger et al., Proc. Natl. Acad. Sci. USA 74 (1977), 5463-5467).
Example 1
Constructs Harboring Sequence Specific DNA-Endonuclease Expression Cassettes for Expression in E. coli 
Example 1a
Basic Construct
In this example we present the general outline of a vector, named “Construct I” suitable for transformation in E. coli. This general outline of the vector comprises an ampicillin resistance gene for selection, a replication origin for E. coli and the gene araC, which encodes an Arabinose inducible transcription regulator. SEQ ID NO: 7 shows a sequence stretch of “NNNNNNNNNN”. This is meant to be a placeholder for genes encoding the different versions of the sequence specific DNA-endonuclease. The different genes can be expressed from the Arabinose inducible pBAD promoter (Guzman et al., J Bacteriol 177: 4121-4130(1995)), the sequences of the genes encoding the different nuclease versions are given in the following examples.
The control construct, in which the placeholder is replaced by the sequence of I-SceI (SEQ ID NO: 8), was called VC-SAH40-4.
Example 2
E. coli—Plasmids Encoding Stabilized Versions of the Nuclease
Different destablizing sequences could be identified in the aminoacid sequence of I-SceI.
Among them a weak PEST sequence at the C-terminus, which comprises amino acid residues 228 to 236 and a N-terminal sequence which shows similarity to a KEN motif (Pfleger and Kirschner, Genes and Dev. 14:655-665 (2000)). According to the N end rule, the second amino acid residue of I-SceI confers instability to the protein.
To test the effect of those sequences on the stability of the nuclease, different versions of I-SceI were generated by PCR, that lack amino acids from the N-terminus, 9 amino acids from the C-terminus or both. Those constructs were expressed from “Construct I”, described in Example 1a). Therefore the placeholder was replaced by various sequences, encoding the versions of the nuclease (shown in SEQ ID NO: 2, 3, 5). The plasmids were called VC-SAH43-8 (C terminal shortened I-SceI) and VC-SAH42-13 (NLS-C terminal shortened I-SceI), VC-SAH44-32 (N terminal shortened I-SceI, SEQ ID NO: 21) and VC-SAH45-3 (N- and C-terminal shortened I-Sce, SEQ ID NO: 22)
According to the N end rule, all these constructs carry the stabilizing second amino acid residue G. To test the effect of the second amino acid on protein stability, also versions with the native, destabilizing residue of I-SceI are generated. The resulting plasmids were called VC-SAH105 and VC-SAH106.
Additional deletions of the C terminus were generated:
Single amino acid residues were successively removed from the C terminus. These variants are summarized in Table 3) and were tested for their activity in E. coli. 
In addition potential PEST sequences were found in I-SceI and analyzed by introduction of single amino acid exchanges. These variants are summarized in Table 3) and were tested for their activity in E. coli.









TABLE 3






vector name
nuclease variant








VC-SAH151-2
NLS I-Scel -1



VC-SAH152-6
NLS I-Scel -2



VC-SAH153-6
NLS I-Scel -3



VC-SAH154-1
NLS I-Scel -4



VC-SAH155-1
NLS I-Scel -5



VC-SAH156-3
NLS I-Scel -6



VC-SAH157-1
NLS I-Scel -7



VC-SAH158-2
NLS I-Scel -8



VC-SAH159-3
NLS I-Scel -10



VC-SAH160-1
NLS I-Scel -11



VC-SAH161-1
NLS I-Scel -12



VC-SAH162-2
NLS I-Scel -13



VC-SAH163-1
NLS I-Scel 1-218



VC-SAH164-2
NLS I-Scel 1-202



VC-SAH165-3
NLS I-Scel 1-187



VC-SAH166-1
NLS I-Scel 1-169



VC-SAH167-1
NLS I-Scel 1-155



VC-SAH190-4
I-Scel L74K



VC-SAH191-3
I-Scel Y75H



VC-SAH192-3
I-Scel Q77K



VC-SAH193-3
I-Scel E130K



VC-SAH194-1
I-Scel T134H



VC-SAH195-2
I-Scel Y199H



VC-SAH196-2
I-Scel M203K



VC-SAH197-2
I-Scel Y205H



VC-SAH198-1
I-Scel S230K









Example 3
Cotransformation of DNA Endonuclease Encoding Constructs and Constructs Harbouring Nuclease Recognition Sequences in E. coli 
Plasmids VC-SAH44-32, VC-SAH43-8, VC-SAH42-13, VC-SAH45-3 and VC-SAH40-4 (described in Example 2) were individually cotransformed with the target vector VC-SAH6-1 or the control vector VC-SAH7-1 in E. coli. The same is done with VC-SAH105 and VC-SAH106 and the vectors summarized in Table 3.
Example 4
Demonstration of the Endonuclease Activity in E. coli 
The versions of I-SceI described in Example 2 were tested for their activity
Cotransformants which carry the combination of two plasmids, one encoding a nuclease or a and the other one harboring the nuclease target site were grown over night in LB with Ampicillin, Kanamycin and Glucose to repress the pBAD promoter. The cultures were diluted 1:100 and grown until they reached OD600=0.5. The expression of the nuclease was induced by addition of Arabinose for 3 to 4 hours. The pBAD promoter is described to be dose dependent (Guzman 1995), therefore the culture was divided in different aliquots and protein expression was induced with Arabinose concentrations varying from 0.2% to 0.0002%. 5 μl of each aliquot were plated on LB solid media, supplemented with Ampicillin and Kanamycin. The plates were incubated over night at 37° C. and cell growth was analyzed semi quantitatively. Active nuclease fusions did cut the constructs, which harbor the target site. This led to the loss of Kanamycin resistance. Therefore, activity of the fusion protein was observed due to the lost ability of the cotransformants to grow on Kanamycin containing medium.
Results:
VC-SAH43-8 (C terminal shortened I-SceI) and VC-SAH42-13 (NLS-C terminal shortened I-SceI) were very active, they cut the target site even in the absence of the inducer Arabinose. Cell growth of these cotransformants was observed only in the presence of Glucose, which further represses the pBAD promoter. So in the cases of VC-SAH43-8 and VC-SAH42-13 the low amount of I-SceI protein produced due to the basal expression from the pBAD promoter was sufficient to cut the target plasmid.
The results are simplified and summarized in Table 4 ++ and + represent very strong and strong growth, which indicates no or little activity of the expressed nuclease towards the respective target site. − and −− represent reduced or no growth, which indicates high or very high activity of the nuclease towards the respective target site.







TABLE 4







I-Scel variants: E. coli growth assay indicates endonuclease


activity against the respective target sites.












VC-SAH6-1
VC-SAH7-1


nuclease variant

(I-Scel site)
(control)





VC-SAH40-4
I-Scel
+
++


VC-SAH43-8
C term shortI-Scel (-9)
−
+


VC-SAH42-13
NLS -C term short I-Scel
−
+



(-9)




VC-SAH151-2
NLS I-Scel -1
−
++


VC-SAH152-6
NLS I-Scel -2
−
++


VC-SAH153-6
NLS I-Scel -3
−
++


VC-SAH154-1
NLS I-Scel -4
−
++


VC-SAH155-1
NLS I-Scel -5
−
++


VC-SAH156-3
NLS I-Scel -6
−
++


VC-SAH157-1
NLS I-Scel -7
−
+


VC-SAH158-2
NLS I-Scel -8
−
+


VC-SAH159-3
NLS I-Scel -10
−
+


VC-SAH160-1
NLS I-Scel -11
++
++


VC-SAH161-1
NLS I-Scel -12
++
++


VC-SAH162-2
NLS I-Scel -13
++
++


VC-SAH163-1
NLS I-Scel 1-218
++
++


VC-SAH164-2
NLS I-Scel 1-202
++
++


VC-SAH165-3
NLS I-Scel 1-187
++
++


VC-SAH166-1
NLS I-Scel 1-169
++
++


VC-SAH167-1
NLS I-Scel 1-155
++
++









Example 5
Transformation of S. cerevisiae 
S. cerevisiae cells are grown in 10 ml YEPS over night and then diluted 1:10. This culture is then grown until it reaches OD600=0.5. The cells are pelleted and resuspended in 15 ml of sterile water twice, pelleted again and resuspended in 1 ml sterile water. This cell suspension is aliquoted a 100 μl and pelleted again. On ice, 240 μl 50% PEG4000, 36 μl 1M LiAc, 20 μl salmon sperm DNA (5 mg/ml) (5 minutes 100° C., then 10 minutes on ice) and 6 μg plasmid in 64 μl water are added. The suspension is incubated at 42° C. for 45 minutes and put on ice for 30 seconds. Cells are pelleted and resuspended in 500 μl water, of which 200 μl are plated on selective media lacking methionine. The plates are incubated at 30° C. for 3 to 4 days. Single colonies can be chosen for further analysis.
Example 6
Constructs Harbouring Stabilized Versions of the Nuclease for Expression in S. cerevisiae 
The sequences described in Example 2 are cloned in the vector pGBT9-3H/B (Tirode et al 1997, J Biol Chem 272:22995-22999) under the control of the MET25 promoter, which is repressed in the presence and active in the absence of methionine.
Example 7
Demonstration of the Endonuclease Stability in S. cerevisiae 
Protein expression is induced by growing the transformants on medium lacking methionine.
Whole protein extract of the different transformants is generated and tested for the abundance and amount of I-SceI by Western blot analysis. Pulse chase experiments are done with the use of Cycloheximide and MG132, to determine the in vivo half life of the different versions.
Example 8
Constructs Encoding Stabilized Versions of the Nuclease for Expression in A. thaliana 
Example 8a
Constructs for Demonstration of the Endonuclease Activity by Crossing Plants Expressing the Nuclease with Plants Carrying a T-DNA with the Respective Target Site
All constructs showing activity in Table 4 are valuable for beeing tested, the following Examples will concentrate on the C terminal shortened version of I-SceI. Different plasmids were generated, where the placeholder of “Construct IV” (SEQ ID No: 13) is replaced by different sequences, encoding the C terminal shortened version of I-SceI, in combinations with or without stabilizing G as second amino acid residue, and with or without NLS. Most favourable are nuclease variants encoded by the constructs VC-SAH151-2, VC-SAH152-6, VC-SAH153-6, VC-SAH 154-1, VC-SAH 155-1, VC-SAH 156-3.
Example 8b
Constructs for Demonstration of the Endonuclease Activity by Transforming these Constructs in Plants already Carrying a T-DNA with the Respective Target Site
In this example we present the general outline of a binary vector, named “Construct VI” (VC-SCB697)suitable for plant transformation. This general outline of the binary vector comprises a T-DNA with a nos-promoter::nptII::nos-terminator cassette, which enables selection on kanamycin, when integrated into the plant genome. SEQ ID NO: 23 (VC-SCB697) shows a sequence stretch of “NNNNNNNNNN”. This is meant to be a placeholder for genes encoding versions of I-SceI.
Different plasmids were generated, where the placeholder is replaced by different constructs, consisting of the C terminal shortened version of I-SceI: VC-SAH124-3 (NLS-I-SceI C term shortened, G) (SEQ ID NO:5), VC-SAH125-2 (I-SceI C term shortened, G), (SEQ ID NO:3), VC-SAH122-7 (I-SceI, G) (SEQ ID NO:2) and VC-SAH123-3 (NLS-I-SceI, G), see Example 2 (As a control I-SceI without the stabilizing G as second amino acid residue was used: VC-SCB697-3). All constructs showing activity in Table 4 are valuable for testing, most favourable are nuclease variants encoded by the constructs VC-SAH151-2, VC-SAH152-6, VC-SAH153-6, VC-SAH 154-1, VC-SAH 155-1, VC-SAH 156-3.
Identical plasmids are generated without the stabilizing G as second amino acid residue.
Example 9
Transformation of Constructs Encoding Stabilized Versions of the Nuclease into A. thaliana 
The plasmids described in Example 8b were transformed in A. thaliana lines carrying the T-DNA of VC-SCB583-40 (SEQ ID NO: 24).
The constructs described in Example 8a) are transformed in wild type plants.
Example 10
Monitoring Activity of the Stabilized Nucleases
Example 10a
By Crossing
The activity of the different versions of I-SceI is monitored by crossing sequence-specific DNA endonuclease expressing lines and lines harbouring constructs with recognition sequences. The recognition sequences are surrounded by a partial uidA (GUS) gene (called “GU”) and another partial uidA gene (called “US”). The partially overlapping halves of the GUS gene (GU and US) are non-functional, but as a result of I-SceI activity on the target site a functional GUS gene will be restored by homologous intrachromosomal recombination (ICHR). This can be monitored by histochemical GUS staining Jefferson et al. (1987) EMBO J 6:3901-3907).
To visualize I-SceI activity, transgenic lines of Arabidopsis harbouring the T-DNA of the plasmids described in Example 9a) are crossed with lines of Arabidopsis harbouring the T-DNA of construct VC-SCB734-4. F1 seeds of the crosses are harvested. The seeds are surface sterilized and grown on medium A supplemented with the respective antibiotics and/or herbicides. 3-4 old seedlings are harvested and used for histochemical GUS staining. The amount of blue areas is an indicator of tissues/parts of tissues in which ICHR occurred in crosses and therefore for I-SceI activity.
Example 10b
By Supertransformation
The activity of the different versions of I-SceI was monitored by transforming lines harbouring constructs with recognition sequences with plasmids harbouring an expression cassette with different versions of the stabilized I-SceI. The recognition sequences are surrounded by a partial uidA (GUS) gene (called “GU”) and another partial uidA gene (called “US”). The partially overlapping halves of the GUS gene (GU and US) are non-functional, but as a result of I-SceI activity on the target site a functional GUS gene will be restored by homologous intrachromosomal recombination (ICHR). This can be monitored by histochemical GUS staining Jefferson et al. (1987) EMBO J 6:3901-3907).
To visualize I-SceI activity, transgenic lines of Arabidopsis harbouring the T-DNA of construct pCB583-40 were transformed with plasmids described in Example 8b). F1 seeds were harvested, surface sterilized and grown on medium A supplemented with the respective antibiotics and/or herbicides. F1 plants were analyzed for single copy integration of the nuclease construct and selfed. F2 plants were grown on medium A without selection pressure. The T-DNA encoding the nuclease is also encoding dsRed. Due to segregation dsRed-free and therefore nuclease-free plants were selected under UV light. Seedlings with 4 leafes were harvested and used for histochemical GUS staining. Blue seedlings represent a homologous recombination event, that has occurred in the previous generation. For each construct 3 to 5 independend lines were analyzed, up to 96 seedlings were stained. The number of blue seedlings is an indicator for I-SceI activity.
Results:
In summary, I-SceI, I-SceI+G and NLS-I-SceI+G resulted between 30%-41% blue plants. Whereas the expression of the C terminal shortened versions encoded by VC-SAH124-3 and VC-SAH125-2 resulted in approximately 60% blue seedlings.
A positive GUS signal represents an ICHR event, due to I-SceI activity. The nuclease can also produce a cut, which might not be repaired by ICHR but by illegitimate recombination. This event will lead to the destruction of the I-SceI recognition seguence and to a non-functional GUS gene. In this case I-SceI activity can not be monitored by the blue staining. To further analyze the white seedlings obtained in this assay, a PCR reaction amplifying the halves of the GUS gene (GU and US) was performed. The amplicons were subjected to I-SceI digestion to detect the presence or absence of the target sequence. The absence of the target site represents I-SceI activity in the previous generation. In summary, the C terminal shortened I-SceI variants resulted in 1 out of 88 tested T2 plants with an intact I-SceI site. In contrast I-SceI encoded by the construct VC-SCB697-3 resulted in 14 out of 48 tested plants which still harbored an uncut I-SceI site.
The Cterminal shortened versions encoded by VC-SAH124-3 and VC-SAH125-2 gave rise to a T2 generation in which in almost all individuals show the result of I-SceI activity.

## Claims

1. An optimized endonuclease comprising an amino acid sequence having at least 92% sequence identity to the amino acid sequence of SEQ ID NO: 1 or 2, wherein said optimized endonuclease does not comprise the amino acid sequence TISSETFLK (SEQ NO: 31) at its C-terminus and has a higher capability to induce homologous recombination in comparison to an endonuclease having an identical amino acid sequence but comprising the amino acid sequence TISSETFLK (SEQ ID NO: 31) at its C-terminus.

2. The optimized endonuclease of claim 1, comprising the amino acid sequence of SEQ ID NO: 3 or 5.

3. The optimized endonuclease of claim 1, which is an engineered endonuclease.

4. The optimized endonuclease of claim 1, wherein the amino acid sequence TISSETFLK (SEQ ID NO: 31) at its C-terminus has been deleted by deleting 1, 2, 3, 4, 5, 6, 7, 8 or 9 amino acids of its C-terminus to create the optimized endonuclease.

5. The optimized endonuclease of claim 1, comprising an amino acid sequence having at least 92% amino acid sequence identity to the amino acid sequence of SEQ ID NO: 1 or 2, and comprising a mutation at a position corresponding to position 229 of the amino acid sequence of SEQ ID NO: 1.

6. The optimized endonuclease of claim 1 fused to:
a) at least one zinc finer domain;
b) at least one repeat unit derived from a transcription activator-like (TAL) effector; or
c) at least one zinc finger domain and at least one repeat unit derived from a transcription activator-like (TAL) effector.

7. The optimized endonuclease of claim 1, further comprising a SecIII or SecIV secretion signal.

8. An isolated polynucleotide comprising a polynucleotide sequence which codes for the optimized endonuclease of claim 1.

9. The isolated polynucleotide of claim 8, wherein the polynucleotide sequence:
a) is codon optimized,
b) has a low content of RNA instability motifs,
c) has a low content of codon repeats,
d) has a low content of cryptic splice sites,
e) has a low content of alternative start codons,
f) has a low content of restriction sites,
g) has a low content of RNA secondary structures, or
h) has any combination of a), b), c), d), e), f), or g).

10. An expression cassette comprising the isolated polynucleotide of claim 8 in functional combination with a promoter and a terminator sequence.

11. A vector, host cell, or non-human organism comprising:
a) an isolated polynucleotide comprising a polynucleotide sequence coding for the optimized endonuclease of claim 1;
b) an expression cassette comprising the isolated polynucleotide of a) in functional combination with a promoter and a terminator sequence; or
c) combination of a) and b).

12. The non-human organism of claim 11, wherein the non-human organism is a plant.

13. A method for homologous recombination of polynucleotides comprising:
a) providing a cell competent for homologous recombination;
b) providing a polynucleotide comprising a DNA recognition site of an optimized endonuclease flanked by a sequence A and a sequence B;
c) providing a polynucleotide comprising sequences A′ and B′, which are sufficiently long and homologous to sequence A and sequence B, to allow for homologous recombination in said cell;
d) providing the optimized endonuclease of claim 1, or an expression cassette comprising a polynucleotide encoding said optimized endonuclease in functional combination with a promoter and a terminator sequence;
e) combining b), c) and d) in said cell; and
f) detecting recombined polynucleotides of the polynucleotides of b) and c), or selecting for or growing cells comprising recombined polynucleotides of the polynucleotides of b) and c).

14. The method of claim 13, wherein upon homologous recombination a polynucleotide sequence in the competent cell of step a) is deleted from the genomes of the cells of step f).

15. A method for targeted. mutation of a polynucleotide comprising:
a) providing a cell comprising a. polynucleotide comprising a DNA recognition site of the optimized endonuclease of claim 1;
b) providing the optimized endonuclease of claim 1, or an expression cassette comprising a polynucleotide encoding said optimized endonuclease in functional combination. with a promoter and a terminator sequence, wherein said optimized endonuclease is able to cleave said DNA recognition site;
c) combining the polynucleotide of a) and the optimized endonuclease of b) in said cell; and
d) detecting a mutated polynucleotide, or selecting for or growing cells comprising a mutated polynucleotide.

16. The method of claim 13, wherein the optimized endonuclease and the DNA recognition site are combined in at least one cell via crossing of organisms, transformation, or transport mediated via a SecIII or SecIV peptide fused to the optimized endonuclease.

17. The optimized endonuclease of claim 1, wherein said optimized endonuclease comprises an amino acid sequence having at least 95% sequence identity to the amino acid sequence of SEQ ID NO: 1 or 2.