Patent Application
20250051789
Submitted as part of this patent application is a Sequence Listing filed as an XML file named UEALG1-0001USC1-SeqList_ST26.xml having a file size of 90,000 bytes and generated on May 16, 2024, the content of which is hereby expressly incorporated by reference in its entirety.
The present invention relates to methods, reagents and compositions for providing more accurate and reliable genetic modification. The invention further provides methods, reagents and compositions for in vivo genetic modification of the genome of a non-animal cell or organism and selection for modified clones/plants. Furthermore, the present invention relates to uses of the said methods, reagents and compositions for introducing desirable traits to non-animal organisms or ameliorating or removing non-desirable traits in these organisms including in the treatment of diseases and production of transgenic organisms.
In recent times genetic modification by way of random mutagenesis has given way to directed mutagenesis of particular nucleotide sequences using sequence-specific protein complexes.
Examples of such protein complexes include zinc-finger nucleases (ZFN), transcription activator-like effector nucleases (TALENs), complexes derived from the CRISPR-Cas9 system of Streptococcus pyrogenes and other bacteria, and CRISPR-Cpf1.
ZFNs and TALENs are both protein nucleases whose protein structure allows them to interact with and recognise a particular DNA sequence before cutting the DNA at a defined location. Thus cutting a particular DNA sequence requires a uniquely designed ZFN or TALEN protein.
In contrast, the CRISPR-Cas9 and CRISPR-Cpf1 systems use a single protein whose activity is directed by an RNA cofactor whose nucleotide sequence defines the location that the endonuclease will act at to produce a double strand break.
Thus, all of these protein complexes act by making a DNA double strand break at a predefined DNA sequence. This double strand break is then normally repaired by the non-homologous end joining (NHEJ) pathway.
Repair by NHEJ is highly efficient and rapid but is more error-prone than the alternative pathway for repair of DNA double-stranded breaks which is homology-directed repair (HDR). Consequently, a proportion of NHEJ pair of events will cause insertion or deletion of nucleotides at the break site. Such insertion or deletion events are known as ‘indels’.
Alternatively, larger genetic modifications are enabled by the presence of a donor DNA molecule in the vicinity of an artificially-created DNA double-stranded break. In this instance HDR of the induced DSB causes repair of the DSB with using the sequence of the donor molecule. In this way specific modifications can be made and short sequence insertions are also possible. One example of such a donor and a vector for producing large amounts of such donor molecules is disclosed in WO 2010/084331.
Homologous recombination proceeds in several distinct stages: the earliest step is processing of the DNA end to produce 3′ single-stranded DNA (ssDNA). Following 5′ strand resection, the 3′ ssDNA is bound by RecA-type recombinases that catalyze homologous pairing and DNA strand exchange. The 3′ end then primes DNA synthesis, and resolution of Holliday junctions or strand annealing between newly-synthesized ends results in repair of the initial DSB (Seitz et al. 2001, PMID: 11677683).
However, the efficiency of genetic modification using homology-dependent recombination (HDR) is low because most repair of double strand breaks proceeds via the more rapid NHEJ pathway.
Furthermore, while the above-mentioned protein complexes are directed to specific sequences their endonuclease activity has been known to act at other sites. Such “off-site breaks” are particularly a problem as NHEJ is more error prone.
Thus, there exists a need for alternative and preferably improved methods and reagents for sequence-specific modification of nucleic acid sequences and of DNA sequences in particular. Furthermore, there is a need for techniques and reagents that more reliably and efficiently yield the desired genetic modification. Additionally, there is a need for techniques and reagents that reliably allow insertion of longer DNA sequences at a pre-defined locus.
An object of the present invention is to provide reagents and techniques for using these reagents that offer alternatives and preferably allow more reliable, efficient and accurate modification and/or mutation of a target genome at specific loci within the genome.
There are provided herein proteins and protein-nucleic acid complexes that provide improved transformation efficiencies and methods for carrying out such transformations. Furthermore the methods, reagents and compositions herein may be used for introducing desirable traits to plants, algae, bacteria and other non-animal organisms or ameliorating or removing non-desirable traits in these organisms including in the treatment of diseases.
Targeting of donor DNA to the target is a critical factor for homology-dependent recombination (HDR). A number of methods have been developed for donor DNA tethering to the target (Sharma & Mclaughlin, 2002, doi: 10.1021/ja020500n; Aird et al., 2018, doi: 10.1038/s42003-018-0054-2; Savic et al., 2018, doi: 10.7554/eLife.33761). Interestingly, covalent linking of donor DNA to cas9 fusion protein increases efficiency of homology-dependent recombination by 24-30 fold, as indicated by fusion of HUH endonucleases to cas9 (Aird et al., 2018, doi: 10.1038/s42003-018-0054-2) or cas9-SNAP-tag domain fusion (Savic et al., 2018, doi: 10.7554/eLife.33761).
Tethering of proteins to RNAs by bacteriophage proteins has been established for decades (Baron-Benhamou et al., 2004, doi: 10.1385/1-59259-750-5-135; Coller & Wickens, 2007, doi: 10.1016/S0076-6879(07)29014-7; Keryer-Bibens et al., 2008, doi: 10.1042/BC20070067; Tsai et al., 2011, doi: 10.1074/mcp.M110.007385), and such approaches could be also utilised for tethering of donor DNA by DNA binding proteins fused to bacteriophage coat proteins recognising specific stem-loop RNA structures. A number of stem-loops and bacteriophage coat proteins are available for tethering, such as MS2 stem loop-MS2 coat protein (Peabody, 1993, PMID: 8440248), PP7 stem loop-PP7 coat protein (Lim & Peabody, 2002, PMID: 12364592), B-box stem loop-lambda N coat protein (Keryer-Biben et al., 2008, doi: 10.1042/BC20070067).
Tethering customized sgRNA from CRISPR with the bacteriophage coat protein-binding RNA stem-loop was described, where stem-loop RNA structure were introduced inside or at the 3′ end of sgRNA and a potential protein of interest was fused to bacteriophage coat protein (Konenmann et al., 2015, doi: 10.1038/nature14136; Nowak et al., 2016, doi: 10.1093/nar/gkw908; Park et al., 2017, doi: 10.1371/journal.pone0179410; Anton et al., 2018, doi: 10.1093/biomethods/bpy002) for site-specific visualization of genomic elements, transcriptional regulation and epigenetic manipulation.
The tethering of donor DNA to the target is, however, technically challenging, as (i) single-stranded linear DNA (SSIDNA) should be produced in vitro, (ii) ssIDNA delivered to cells is less efficient then dsDNA, (iii) ssIDNA is not stable in vivo and is subject to rapid endonuclease degradation, and as result, (iv) low concentration of donor DNA around the targeted locus significantly reduces HDR.
Thus delivery of ssDNA to cells is challenging. ssDNA is difficult to deliver technically because ssDNA is not naturally imported into cells and is rapidly degraded. Advantageously, the present invention addresses this problem by delivering dsDNA and then producing ssDNA in the desired location from this dsDNA.
To address these issues we utilise e.g. HUH rep proteins from bacteriophages, circoviruses, geminiviruses, rolling circle transposons from bacteria or plants (such as helitrons) preferentially active in plant cells for rolling circle replication, and replicative donor vector containing double-stranded donor DNA flanked by one or two viral origins of replication.
Modification of the target is significantly improved by producing ssDNA in vivo and causing it to accumulate in the vicinity of the locus to be modified. Accumulating the ssDNA in the vicinity of the locus to be modified means that it is available for use in HDR processes for a longer period, which advantageously promotes HDR. Additionally, amplification of the ssDNA copy number allows more of the ssDNA moiety to accumulate close to the locus of interest, which, as noted above, promotes more efficient editing of the target locus.
Our approach allows addressing all problems indicated above by one or more or all of:
Single-stranded donor DNA can be produced from a linear dsDNA donor replicative vector with one origin of replication fused to the 5′ end of donor DNA, or from a linear or circular dsDNA replicative vector where a donor DNA fragment is flanked by origins of replication on both 5′ and 3′ ends.
Accordingly, the present invention provides a nucleic acid encoding a first fusion protein comprising an endonuclease or bacteriophage coat protein domain and a binding domain for an origin of replication.
Functionally significant domains or regions of different proteins or polypeptides may be combined for expression from an encoding nucleic acid as a fusion protein. For example, particularly advantageous or desirable properties of different proteins or polypeptides may be combined in a hybrid protein, such that the resultant expression product may include fragments of various parent proteins or polypeptides.
In the fusion proteins described herein the domains of the fusion proteins are preferably joined together via linker peptides. The particular choice of linker will depend on the constituent domains of the fusion protein. The suitability and choice of appropriate linker peptides is discussed in Chen et al. (Adv Drug Deliv Rev. 2013; 65 (10): 1357-1369).
The endonuclease may cleave a target nucleic acid molecule in a sequence specific manner. The sequence specific cleavage of the nucleic acid molecule may be double or single stranded (including ‘nicking’ of duplexed nucleic acid molecules; double stranded cleavage may yield blunt ends or overhanging termini (5′ or 3′ overhangs)). The sequence specific nuclease preferably acts as a monomer but may act as a dimer or multimer. For instance a homodimer wherein both monomers make single strand nicks at a target site can yield a double-strand break in the target molecule. Preferably the cleavage event makes a double-stranded break in the target molecule.
Examples of sequence-specific endonucleases include zinc-finger nucleases (ZFN), transcription activator-like effector nucleases (TALENs), complexes derived from the CRISPR-Cas9 system of Streptococcus pyogenes and other bacteria, and CRISPR-Cpf1.
A nucleic acid molecule may comprise double-or single-stranded DNA or RNA. The nucleic acid molecule may also comprise a DNA-RNA duplex. Preferably the nucleic acid molecule is double-stranded DNA. Preferably the cleavage event makes a double-stranded DNA break in the target molecule.
Preferably the endonuclease is a DNA endonuclease and most preferably this is Cas9. This may be Cas9 from Streptococcus pyrogenes or a homologous or functionally equivalent enzyme from another bacteria.
The fusion protein may comprise an endonuclease and a component of the replication initiation complex or replication complex.
The components of the replication initiation complex or replication complex are necessarily associated with origins of replication and may be covalently attached thereto or to the elongating nucleic acid molecule. Suitably the origin of replication is derived from bacteriophages, eukaryotic viruses and various types of transposons, maintaining rolling circle replication function in the targeted cell. The endonuclease for specific origin of replication may first produce a stem loop at dsDNA origin fused to donor, nick single-stranded DNA at the stem loop followed by formation of a covalent phosphotyrosine intermediate, whereby the 5′ end of the DNA strand becomes linked to a specific tyrosine in the HUH-protein. Most suitably for application in plants are geminivirus, plant rolling circle transposons or another family of the rep genes.
Geminivirus Rep protein (GV-Rep) binds to the geminivirus origin of replication and thus becomes covalently linked to the ssDNA strand of donor DNA produced by rolling circle replication initiated at the origin of replication. Thus the newly replicated donor DNA molecule is covalently linked to the first fusion protein and is necessarily brought into close proximity to the site of the double-stranded DNA break caused by the endonuclease.
The invention further provides a nucleic acid encoding a second fusion protein comprising a 5′ to 3′ DNA exonuclease domain and an RNA binding domain. As an alternative to the second fusion protein, the invention also provides for the use of a 5′ to 3′ DNA exonuclease without an RNA binding domain.
Both Zalatan et al. (Cell (2015) 160, 339-350) and the CRISPRainbow system described initially by Ma et al. (Nat Biotechnol. 2016 Apr. 18. doi: 10.1038/nbt.3526) utilise a modified sgRNA containing 3′ RNA hairpin aptamers that bind uniquely labelled RNA binding proteins (SEQ ID NO: 16). Thus the sgRNA is functionalised so that it can be used to locate fusion proteins comprising binding domains for the aptamers in association with the sgRNA and hence the endonuclease it is associated with.
The action of the second fusion protein may be for inhibition of NHEJ during transformation of a cellular genome so as to promote HDR. The effect of such 5′ to 3′ resection on DNA double-strand breaks is to suppress religation of DNA breaks (i.e. by blocking NHEJ), by producing a substrate that is less suitable for NHEJ but is significantly more suitable for HDR. The action of the second fusion protein may be for inhibition of NHEJ during transformation of a genome so as to promote HDR.
The exonuclease may be a dsDNA exonuclease. The exonuclease may be lambda exonuclease (λ-exo). Lambda exonuclease (SEQ ID NO: 15) is a 5′ to 3′ exonuclease and is involved in recombination, double-strand break repair, the MMS2 error-free branch of the post replication repair (PRR) pathway and DNA mismatch repair.
Lambda exonuclease (λ exo) plays an important role in the resection of DNA ends for DNA repair. Lambda exonuclease is a 5′-3′ exonuclease that progressively digests one strand of a duplex DNA molecule to generate a 3′-single stranded-overhang (Carter& Radding, 1971, PMID: 4928646). Because of its robust properties and low cost, λ exo is widely used in multiple biotechnology applications, such as genetic engineering using homologous recombination.
In the complex with DNA, λ exo unwinds two bases at the 5′ end of the substrate strand to pull it into the reaction centre. It hydrolyses double-stranded DNA (dsDNA) 130 times faster than single-stranded DNA (ssDNA) (Little, 1967, PMID: 6017737). A DNA duplex with a 5′ phosphorylated blunt or recessed end is the appropriate substrate for λ exo, while the digestion rate of a dsDNA with a 5′ hydroxyl end or a 5′ phosphorylated overhang is significantly slower (Mitsis & Kwagh, 1999, PMID. 10454600, Tongbo et al., 2018, doi: 10.1093/nar/gkyl54).
Exonucleases with 5′-3′ activities are presented in other organisms. The Cas4 protein is one of the core CRISPR-associated (Cas) proteins implicated in the prokaryotic CRISPR system for antiviral defence. The Cas4 protein is a 5′ to 3′ single stranded DNA exonuclease in vitro and it is involved in DNA duplex strand resection to generate recombinogenic 3′ single stranded DNA overhangs (Zhang et al., (2012) https://doi.org/10.137/journal.pone.0047232).
RecJ from Deinococcus radiodurans, a member of DHH family proteins, is the only 5′ nuclease involved in the RecF recombination pathway, providing the resection of DNA strand with a 5′ end at double-strand breaks as an essential step in recombinational DNA repair. As a processive nuclease. RecJ only degrades ssDNA in a 5′-3′ direction but nuclease alone is capable of digesting DNA with only 5′-ssDNA overhang (Jiao et al., 2012, doi. 10.1016/j.dnarep.2011.11.008).
Genetic studies in Saccharomyces cerevisiae show that end resection takes place in two steps. Initially, a short oligonucleotide tract is removed from the 5′ strand to create an early intermediate with a short 3′ overhang by the highly conserved Mre11-Rad50-Xrs2 (MRX) complex and Sae2. Then in a second step the early intermediate is rapidly processed generating an extensive tract of ssDNA by the exonuclease Exo1 and/or the helicase-topoisomerase complex Sgs1-Top3-Rmi1 with the endonuclease Dna2 (Mimitou& Symington, 2011, doi: 10.1016/j.dnarep.2010.12.004).
In archaea, such as Pyrococcus furiosus the end resection is executed by the bipolar helicase HerA and the 5′-3′ exonuclease NurA (Hopkins&Paull, 2008, doi: 10.1016/j.cell.2008.09.054). Thus, loading or activation of HerA-NurA complex promotes resection of the 5′ strand of the double-stranded DNA break (DSB) and initiate of strand invasion.
For more information on enzymes involved in 5′ end DNA resection and mechanisms of 3′ DNA ends generation in the three domains of life see Blackwood et al., 2013, (doi: 10.1042/BST20120307); Liu&Huang, 2016, (doi: 10.1016/j.gpb.2016.05.002); Raynard et., 2019, (doi/10.1101/gad.1742408); Sharad&You, 2016, (doi: 10.1093/abbs/gmw043); Yin&Petes, 2014, (doi.org/10.1534/genetics. 114.164517).
The invention further provides a nucleic acid encoding a third fusion protein comprising a recombination inducing domain and an RNA binding domain.
The recombination domain may be a protein or polypeptide that interacts with a target or donor nucleic acid molecule in order to catalyse modification of the nucleotide sequence of the target nucleic acid with reference to the nucleotide sequence of the donor nucleic acid molecule.
Modification of the target nucleic acid may be by way of insertion of all or a part of the sequence of the donor nucleic acid molecule or substitution of all or a part of the sequence of the donor nucleic acid molecule for a homologous section of the target nucleic acid molecule. In this way deletions, insertions, frameshift mutations and single nucleotide mutations may be achieved.
The recombination inducing event caused or mediated by the recombination inducing domain may be initiating or catalysing strand exchange between the target and donor nucleic acid molecules.
The recombination domain may be RecA from E. coli or a homologue thereof, Rad51 or a homologue thereof from a plant or another organism, or an annealase from such as bacteriophage λ recombination protein beta (BET; Redβ) or a homologue thereof. Studies of phage lambda in vivo have indicated that bacteriophage λ beta protein can catalyse steps that are central to both the strand annealing and strand invasion pathways of recombination (Matsubara et al., 2013, doi: 10.1371/journal.pone.0078869). A homologous protein in this case may have functional or sequence homology, preferably functional homology.
Preferably the recombination domain is a trimer of RecA (SEQ ID NO: 17) or Rad51 monomers (SEQ ID NO: 18). Most preferably the monomers are joined by peptide linkers. Use of a trimer of monomers for the recombination domain is advantageous because this allows binding of a turn of the nucleic acid helix in order to more efficiently initiate strand exchange and hence HDR.
The invention further provides a nucleic acid encoding a fourth fusion protein comprising a domain comprising an inhibitor of the mismatch repair pathway; and an RNA binding domain.
MSH2 and MSH6 are proteins involved in base mismatch repair and the repair of short insertion/deletion loops. The MSH2 dominant-negative mutant (Sia et al., 2001, doi: 10.1128/MCB.21.23.8157-8167.2001) (SEQ ID NO: 25) competes with MSH2 binding to mismatches thus blocking the ability of the wild-type MSH2 protein to repair these mismatches. A dominant negative allele of MSH6 is also known and may be used in the same way as the dominant negative allele of MSH2 (Bowers et al., 1999, doi: 10.1074/jbc.274.23.16115).
The invention further provides a nucleic acid encoding a fifth fusion protein comprising a domain comprising a Holliday junction resolvase and an RNA binding domain. Suitable resolvases are e.g. a bacteriophage T4 endonuclease VII (T4E7) (SEQ ID NO: 26) a bacteriophage T7 endonuclease I (Babon et al., 2003, doi: 10.1385/MB:23:1:73); CCE1 (SEQ ID NO: 27) a YDC2 resolvase from yeast (Kleff et al., 1992, PMCID:PMC556502; White et al., 1997, doi:10.1128/MCB.17.11.6465); a GEN1 resolvase from human (Ip et al., 2008, doi: 10.1038/nature07470), and an AtGEN1 resolvase from Arabidopsis thaliana (SEQ ID NO: 28), (Bauknecht & Kobbe, 2014, doi: 10.1104/pp.114.237834).
The rearrangement and repair of DNA by homologous recombination involves the creation of Holliday junctions, which are cleaved by a class of junction-specific endonucleases to generate recombinant duplex DNA products.
The formation of DNA joint molecules is a transient process, which usually disrupted at an early stage by anti-recombinogenic helicases such as Srs2, Mph1 or RTEL1 (Gangloff et al., 1994, PMCID: PMC359378; Malkova et al., 2003, PMCID: PMC4493758; Prakash et al., 2009, doi: 10.1101/gad.1737809).
In somatic cells HDR is suppressed by low expression of resolvase and high activities of anti-recombinogenic helicases. The DNA helicase that translocates along single-stranded DNA in the 3′ to 5′ direction displaces annealed DNA fragments and removes Holliday junction intermediates from a crossover-producing repair pathway, thereby reducing crossovers and HDR (Malkova et al., 2003, PMCID: PMC4493758).
In order to improve efficiency of HDR, timely delivery of resolvase to Holliday junctions, formed during donor DNA annealing, may thus be provided to fix the recombination event and translate it into the modification at the target site.
The second, third, fourth and fifth fusion proteins may bind to the RNA component of an RNA-guided endonuclease for use in transformation mediated by the RNA-guided endonuclease. Preferably an RNA component is a tracrRNA molecule or domain for use in transformation using the CRISPR-Cas9 system. Note that reference throughout to a given domain comprising, say, a RNA binding domain includes the given domain both being and comprising that specified domain.
The invention also provides a method of transforming the genome of a non-animal cell comprising the steps of:
Thus the invention provides a system with multiple features that may be used separately or in concert. These features include one or more or all of:
Features (c), (d), (e) and (f) are suitably supplied to the HDR complex by their being provided in the form of the second, third, fourth and fifth fusion proteins, i.e. each comprises a domain that binds to an aptamer engineered to be part of the sgRNA that guides the endonuclease activity of the first fusion protein (e.g. the sgRNA of SEQ ID NO: 16).
The second, third, fourth and fifth fusion proteins each suitably comprises a domain that binds to an aptamer engineered to be part of the sgRNA that guides the endonuclease activity of an RNA-guided endonuclease. Therefore the second, third, fourth and fifth fusion proteins may be used in concert with an RNA-guided endonuclease other than the first fusion protein, such as Cas9 or Cpf1.
Feature (b) may also be provided comprising a domain that binds to an aptamer engineered to be part of the sgRNA that guides the endonuclease activity of an RNA-guided endonuclease.
One advantage flowing from use of any or all of the first, second, third, fourth and/or fifth fusion proteins of the invention is more reliable and efficient genetic modification.
A further advantage is that use of any or all of the first, second, third, fourth and/or fifth fusion proteins of the invention allows for insertion of longer DNA sequences at a locus or loci acted on by a sequence-guided endonuclease that has previously been reported.
The invention also provides a method of modifying the genome of a non-animal organism or cell comprising:
As will be appreciated, the first fusion protein comprises an endonuclease domain and a binding domain for an origin of replication, wherein the binding domain suitably matches, e.g. binds to, the origin of replication of the donor nucleic acid.
Advantageously, the first fusion protein is capable of performing multiple functions. These functions include one or more of, or all of:
Particular advantage(s) are yielded by amplifying donor DNA and/or accumulating this in close proximity to the target: accumulation of donor DNA near the locus of the DNA double-strand break promotes repair of the break by HDR. Providing a greater concentration of donor DNA near the target locus promotes HDR. Without wishing to be bound by theory, this is believed to be because the greater availability of a donor with a section homologous to the target means that the less accurate but quicker NHEJ pathway is not favoured under these conditions.
Non-animal organisms in the context of the present disclosure may be prokaryotes (bacteria and archaea), algae, plants or any other non-animal organism including protists and fungi. Preferably, the non-animal organisms are plants along with any part or propagule thereof, seed, selfed or hybrid progeny and descendants. The plants may be monocot or dicot plants. Suitably the plants are Arabidopsis, tobacco, rice or a transgenic crop plant. Examples of suitable transgenic crop plants include tobacco (Nicotiana tabacum) and other Nicotiana species, carrot, vegetable and oilseed Brassicas, melons, Capsicums, grape vines, lettuce, strawberry, sugar beet, wheat, barley, (corn) maize, rice, soya bean, peas, sorghum, sunflower, tomato, cotton, and potato. The non-animal organisms may be algae.
The donor nucleic acid molecule may comprise:
The replication terminator may be a non-functioning origin of replication that is still capable of terminating replication when a replication fork reaches it. It is optionally omitted if linear dsDNA donor is flanked at 5′ end by viral origin of replication. In a specific example, a geminivirus origin of replication is nicked by the Rep protein at a particular location on a stem loop characteristic of the origin of replication. As long as the stem loop is present and correctly nicked then replication may be terminated at that location. Other sequence elements of the origin are not essential for termination and therefore can be omitted from the replication terminator in this example.
However, the nick at the replication terminator derived from such an origin of replication (in, for instance geminiviruses) may still be competent for religation of the nicked stem loops at the active origin of replication and the downstream terminator/origin of replication. In this way a nucleic acid circle with an active origin of replication is provided and may be actively replicated by rolling circle replication or another mode of replication.
Rolling circle replication of the donor DNA acid molecule has the advantage of providing a large amount of donor DNA nucleic acid. Provision of a relatively large amount of donor nucleic acid molecule means that the probability of the successful transformation is raised.
Although modification in desirable locus of the cells can be introduced, recovery of modified clones or plants from such cells is difficult due to competition between modified and non-modified cells. Regeneration of clones or plants from the population of modified and non-modified cells can be tedious and time-consuming.
The method provides a specific replicative donor vector allowing selection for clones/plants with desirable modification.
Accordingly, also provided by the invention is a selection vector comprising first and second viral origins of replication, wherein the first and second viral origins of replication are arranged to flank a donor DNA fragment; and the donor DNA fragment comprises a selectable marker gene that is fused out of frame.
The first and second viral origins of replication may be arranged to flank a DNA sequence comprising a promoter and a donor DNA fragment, and the donor DNA fragment may comprise a selectable marker gene that is out of frame with the promoter.
One example of the selection vector for introduction of knock out mutation in the cell and recovery of clones or plants on selection media is presented in Example 3 and
The introduced selection vector comprises more generally two viral origins of replication flanking a donor DNA fragment and a selectable marker gene fused in frame with respect to translation of the product giving rise to the effect of the marker. The viral origin of replication at the 5′ end of the donor DNA contains a eukaryotic promoter with an ATG translation codon, fused ‘in-frame’ with donor DNA fragment, linker, selectable marker gene (such as nptII, hygromycin or phosphinotricin resistance genes) terminator (such as the nos terminator), followed by 3′ end viral origin of replication (SEQ ID NO: 29). All sequences introduced after the ATG codon represent one translational unit, generating a selectable marker, e.g. resistance to antibiotic, in this example: kanamycin antibiotic.
In order to introduce a knock out mutation into specific gene, a stop codon/deletion/insertion is introduced in the donor DNA fragment. As the stop codon is introduced into the donor fragment in front of a selectable marker gene, which is preferably nptII, no antibiotic resistance generated by the selection donor vector is observed due to premature termination of translational unit on selection vector.
Recombination of the donor DNA fragment with the target transfers the stop codon to the target sequence, while the DNA fragment without a stop codon from the target replaces the donor fragment in the selection donor vector. As result, the translational unit on the donor vector will be restored, and the vector will be amplified, allowing selection on kanamycin supplemented medium. The cells where translational unit of the donor vector was restored by exchange between donor and target DNA strands during recombination process will be resistant to kanamycin selection, and clones or plants can be recovered from such cells on selection medium.
The methods described herein may comprise introducing a double strand break into the genome in the presence of an exogenous donor nucleic acid molecule comprising a donor nucleic acid sequence as a template for modifying the genome or as an exogenous sequence to be integrated into the genome; a DNA repair mechanism modifies the genome via homology-directed repair (HDR).
The method may further comprise the step or effect of suppressing non-homologous end joining (NHEJ) repair of a DNA double-strand break to promote repair of the break by HDR by expressing in the cell a nucleic acid encoding the second fusion protein or introducing the second fusion protein into the cell.
The methods described herein may comprise introducing a double strand break into the genome in the presence of an exogenous donor nucleic acid molecule comprising a donor nucleic acid sequence as a template for modifying the genome or as an exogenous sequence to be integrated into the genome, and wherein a DNA repair mechanism modifies the genome via homology-directed repair (HDR), the method comprising:
The method may further comprise the steps of:
The method may further comprise the steps of:
The method may further comprise the steps of expressing in the cell two or more nucleic acids encoding the second, third, fourth and fifth fusion proteins or introducing into the cell two or more of the second, third, fourth and fifth fusion proteins, wherein the RNA binding protein domains of the respective fusion proteins bind to different RNA sequences.
In this way the first fusion protein may be using in concert with the second, third, fourth and fifth fusion proteins for transformation of a non-animal cell or organism in concert with an RNA-guided endonuclease.
Expression of the first, second, third, fourth and fifth fusion proteins during a method of modifying the genome as described herein may be via inducible and/or transient expression.
Various methods for introducing nucleic acids encoding the fusion proteins and nucleic acids of the invention are envisaged; these include electroporation and infiltration in order to introduce proteins, DNA and/or RNA. Also envisaged is the use of delivery systems, including liposomes or lipid nanoparticles (LNP), for directly introducing proteins, DNA and/or RNA, preferably by encapsulation of the proteins, DNA and/or RNA therein.
The invention also provides a first fusion protein comprising an endonuclease and a component of the replication initiation complex or replication complex.
The component of the replication initiation complex or replication complex may be also introduced in fusion with bacteriophage coat protein (MS2 coat protein) in combination with stem loops introduced into the sgRNA of CRISPR system.
The invention further provides a second fusion protein comprising a 5′ to 3′ DNA exonuclease domain and an RNA binding domain.
The invention also provides a third fusion protein comprising a recombination inducing domain and an RNA binding domain.
The invention further provides a fourth fusion protein comprising a domain comprising an inhibitor of the mismatch repair pathway and an RNA binding domain.
The invention further provides for use of the first fusion protein, or a nucleic acid encoding the first fusion protein in transformation of a non-animal organism or cell.
The invention further provides for use of the second fusion protein, or a nucleic acid encoding the second fusion protein in transformation of a non-animal organism or cell using an RNA-guided endonuclease.
The invention also provides for use of the first fusion protein, or a nucleic acid encoding the first fusion protein in concert with the second, third and fourth fusion proteins in transforming a non-animal organism or cell using an RNA-guided endonuclease.
The invention provides for use of the first fusion protein, or a nucleic acid encoding the first fusion protein in concert with the second, third, fourth and fifth fusion proteins in transforming a non-animal organism or cell using an RNA-guided endonuclease.
The invention provides for use of the first fusion protein, or a nucleic acid encoding the first fusion protein in concert with combination of any fusion protein(s) (second, third, fourth and/or fifth) dependent on desirable gene modification in transforming a non-animal organism or cell using an RNA-guided endonuclease.
The invention further provides vectors comprising the nucleic acids of the invention. Such vectors may be suitable for modification in vitro or in vivo and selection for modified clones and plants.
Vectors of the invention capable of expressing products encoded on nucleotides of the invention may also be suitable for expression in a host cell or cell-free system. Suitably the host cell may be a cultured plant cell, yeast cell or bacterial cell, e.g. Escherichia coli. Compositions and products of the invention may be obtained by methods comprising expressing such encoded products in a suitable host cell or cell-free system.
The invention also provides the methods, reagents and compositions disclosed herein for use in the treatment of disease in non-animal organisms.
The invention also provides uses of the methods, reagents and compositions disclosed herein for introducing desirable genetic characteristics to non-animal organisms or ameliorating or removing non-desirable genetic characteristics in these organisms.
The invention also provides uses of the methods, reagents and compositions disclosed herein for introducing desirable heritable characteristics to non-animal organisms or ameliorating or removing non-desirable inherited characteristics in these organisms.
Accordingly, the invention also provides non-animal transgenic organisms, transgenic cells thereof and transgenic non-animal cell lines. Organisms which include a transgenic cell according to the invention are also provided.
The invention further provides methods of treating disease or other conditions of non-animal organisms or cells by utilising the methods, reagents and compositions disclosed herein.
The invention is now illustrated in specific embodiments with reference to the accompanying drawings in which:
To assess efficiency of gene targeting in tobacco a set of constructs was prepared for targeting an exogenous uidA gene from E. coli.
Transformations were carried out by infiltration (see method below).
A two base pair deletion was introduced in the uidA gene from E. coli (SEQ ID NO: 2). The modified uidA gene was introduced into tobacco under the cauliflower mosaic virus (CMV) 35S promoter (SEQ ID NO: 1) with a nos terminator (SEQ ID NO: 3) (ALG 492,
The tobacco plants carrying the mutated uidA gene were then co-transformed with a repair donor comprising SEQ ID NO: 4 as part of construct FVLR (
These results demonstrate that gene editing mediated by the Cas9-Rep fusion (experiment (ii)) is significantly more efficient than for the control experiment using cas9 alone.
These results also demonstrate that gene editing mediated by the Cas9-Rep fusion and an exo1-MS2 fusion protein designed to bind to the Cas9-sgRNA complex (experiment (iii)) is yet more efficient than either the control experiment using cas9 alone or experiment (ii) using the Cas9-Rep fusion alone.
Insertion of long DNA sequences into the double-stranded breaks represents a challenge for modification of genomes for different organisms. Here we present an improvement of the insertion efficiency into tobacco genome using a combination of molecules from the invention.
Two targets were chosen for the experiment, namely acetolactate synthase (ALS) and protoporphyrinogen oxydase 1 (PPOX1) genes. Two vectors were designed for insertion at the end of the ALS (SEQ ID NO: 30) and PPOX1 (SEQ ID NO: 31) genes using translational fusion of nptII gene (SEQ ID NO: 32) (
Tobacco plants were transformed using Agrobacterium-mediated method with constructs FTTA and AVPP for insertion in ALS locus, and FTTB and AVPR for PPOX1 locus (
CRISPR/cas9 system is widely used for generation of knock out mutations. However such mutations cannot be controllable as non-homologous end joining (NHEJ) will cause various insertions or deletions of nucleotides at the break site. Such insertion or deletion events are known as ‘indels’.
The invention provides a method for generation of stop codon in the desirable target and selection for the cells/clones/plants using selection donor vector. The selection donor vector can be also designed for both precise deletion and insertion to introduce knock out mutation, if necessary.
A tobacco phytoens desaturase (PDS) gene was chosen for introduction of premature stop codon into one of the gene exons, to cause regeneration of albino plants, as shown by Wang et al., 2010 (doi: 10.1018/j.envexpbot.2009.09.007).
The donor DNA fragment was designed with premature stop codon in the PDS exon (SEQ ID NO: 35) and introduced into the selection donor vector in translational frame with nptII gene (
Agrobacterium-mediated transformation of tobacco was performed with constructs FVTX and AVPS (
We prepared mutated version of cas9-Rep (SEQ ID NO: 37), where both nuclease activities sites were eliminated resulting in so-called dead cas9 nuclease (dCas9-Rep). Although nuclease activities were eliminated, dCas9-Rep still binds to sgRNA and recognises the target. As Rep gene is fused to dCas9, the donor DNA molecule covalently linked to Rep is still tethered to the target and can be annealing with target forming Holliday junctions. Such annealing of donor DNA with target and formation of Holliday junction are suppressed by endogenous helicases. In order to facilitate rapid resolution of Holliday junctions at the target site after annealing of donor DNA, we have co-delivered AVPT vector with resolvase from bacteriophage T4 (T4 exonuclease VII (T4E7)) or AVPU vector with Arabidopsis AtGEN1 resolvase fused to MS2 coat protein to tether it to target site using MS2 stem-loops integrated into sgRNA (
All items are autoclave-sterilised prior to use. Filter sterilize antibiotics to prevent fungal growth, keep antibiotics for plant tissue culture in separate box.
Sterilize plant material: take plants of about 9 cm high which have not started to flower. Cut leaves having a cuticle (4-6 leaves per construct, enough to cut 100 explants), dip in 70% Ethanol and immediately dip in 1% Na-hypochlorite (use a bottle of bleach that is <3 months old because the chlorine gas evaporates), hold leaves with forceps and stir in it for 20 min. Avoid damaging the cuticle otherwise bleach will enter the vascular system. Rinse briefly in sterile water 5-6 times and leave in water until ready to be cut.
Co-cultivation of Agrobacterium with tobacco explants: grow AGLI in LB or L broth with appropriate antibiotics overnight at 28-30° C., the next day re-suspend Agrobacterium in co-cultivation solution so that the final concentration has an OD6oonm of around 0.4-0.6. Place tobacco leaves in co-culture broth and cut squares of 1-1.5 cm×1-1.5 cm with a rounded sterile scalpel using a rolling action. Dip the leaf explants in the Agrobacterium solution with sterile forceps (stored in 100% ethanol, flamed and let to cool prior to touching the leaf tissue) blot on sterile Whatman paper and transfer on non-selective TSM plates (6 explants per plate; need to prepare about 15 plates per construct). Repeat this procedure for each construct, making sure that the scalpel and forceps are dipped in ethanol and flamed between each construct to prevent cross-contamination. Leave for 2 days only for AGLI (3-4 days for other Agrobacterium strains).
Transfer on selective TSM plates: use sterile flamed forceps to pick up and wash explants in 100 ml co-cultivation broth supplemented with Timentin 320 mg/l (one aliquot per construct), shake well, blot on sterile Whatman paper and place the washed explants on selective TSM plates supplemented with appropriate selective antibiotics and Timentin 320 mg/l to kill Agrobacterium.
Shoot regeneration: takes around 1 month to see shoots appear, explants should be transferred onto fresh plates every 10-14 days. Watch out for AGLI recurrent growth, if Timentin is not enough to kill Agrobacterium, add cefotaxime at 250 mg/l.
Root regeneration: Takes around 1 week. Shoots are cut from the explants and place in growth boxes containing TRM supplemented with the appropriate selective antibiotics and Timentin 320 mg/l+cefotaxime 250 mg/l to prevent Agrobacterium recurrent growth. Maintain plants in TRM boxes: sub them every two weeks until ready to be transferred into a glasshouse.
Adaptation to glasshouse conditions: soak peat pellets in sterile water until they swell to normal size and carefully plant one plant per pellet, incubate the plants under 100% humidity conditions in a propagator, gradually opening the little windows until plants adapt to normal atmosphere over several days.
Assay the transgenic plants for GUS activities as described by McCabe et al., (Nature Biotechnology, 1988, 6, 923-926).
Arabidopsis U6A promoter
Arabidopsis AtGEN1 resolvase,
| Number | Date | Country | Kind |
|---|---|---|---|
| 18175623.0 | Jun 2018 | EP | regional |
This application is a continuation that claims the benefit of priority and is entitled to the filing date pursuant to 35 U.S.C. § 120 of U.S. Non-Provisional patent application Ser. No. 15/733,848, filed on Nov. 30, 2020, a U.S. national stage application filed pursuant to 35 U.S.C. § 371 from International Patent Application Serial No. PCT/EP2019/064215, filed on May 31, 2019 which claims the benefit of priority and the filing date of European Patent Application Serial No. 18175623.0, filed on Jun. 1, 2018, the content of each of which is hereby incorporated by reference in its entirety.
| Number | Date | Country | |
|---|---|---|---|
| Parent | 15733848 | Nov 2020 | US |
| Child | 18665659 | US |
