Patent Application
20140373194
The present invention relates generally to RNAi and its use in gene silencing. Furthermore, the present invention relates to methods and constructs for delivering double stranded RNA (dsRNA) to pest organisms.
Targeted inhibition of gene expression has been a long-felt need in biotechnology and genetic engineering. In the last few years, advances in nucleic acid chemistry and gene transfer have inspired new approaches to engineer specific interference with gene expression.
One of these approaches consists of double-stranded RNA inhibition (RNAi) as a tool for controlling gene expression, as described in WO 99/32619 and WO 00/01846. Double-stranded RNA inhibition is based on the introduction of RNA into a living cell to inhibit gene expression of a target gene in that cell. The RNA has a region with double-stranded structure. Double-stranded RNA (dsRNA) has the capability to render genes nonfunctional in a sequence-specific manner. When introduced into cells, dsRNA can activate mechanisms that target the degradation of cognate cytoplasmic mRNAs and thus can effectively silence full gene expression at the posttranscriptional level. RNAi has been observed in many cell types from divergent eukaryotes, including protozoa, fungi, plants, invertebrates, and mammals. Once inside the cells, long dsRNA molecules are cleaved into double-stranded small interfering RNAs (siRNAs) that are 21-25 base pairs in length by an enzyme with RNaseIII-like activity (Dicer). Cleavage into siRNAs is an early step in the RNAi silencing mechanism. Introduction of double-stranded RNA (dsRNA) can elicit a gene-specific RNA interference response in a variety of organisms and cell types.
In plants this technology may be used for instance with the aim of modifying or improving plant resistance towards pathogens and pests. The latter technique may involve the uptake of the dsRNA by pest organisms when feeding on the plants. In delivery by feeding, dsRNA may be distributed to cells from the gut of the feeding organism in the same manner as nutrients. It is also conceivable that dsRNA residing in “infected” cells could undergo successive rounds of cellular exit and re-entry into adjacent “uninfected” cells.
However, delivery of dsRNA to pest organisms by feeding has limits. Difficulties related to the delivery of dsRNA to feeding target organisms are numerous and may for instance involve the need to use very high amounts of dsRNA in order to be effective. Also, dsRNA may easily break down in the plants or during delivery to the target organism. Furthermore, in order to be effective, the dsRNA molecules should efficiently be taken up by the pest and delivered to the correct targeting site in the pest organisms.
Since the advent of double-stranded RNA inhibition there has been recognized a need for specialized constructs designed for site-directed delivery of double-stranded RNA in a pest organism. While there are various methods available for directly and indirectly introducing dsRNA into cells, it is clear that these methods are generally inefficient, and have practical limitation. Therefore, in view of the foregoing, there exists a need to develop tools and methods for the more efficient delivery of dsRNA into pest cells for the purpose of achieving RNAi and to kill or paralyze the pest. The present invention aims to provide improved methods and constructs useful in the delivery of double-stranded RNA in pest organisms, including nematodes, insects and fungi. An object of the present invention is thus to provide dsRNA constructs with improved properties to be effectively taken up in the cells or tissues of the pest species.
Insect, fungal and nematode pests are a major cause of damage to the world's commercially important agricultural crops. Current strategies aimed at reducing crop losses rely primarily on chemical pesticides. Alternatively transgenic crops with intrinsic pest resistance offer a promising alternative and continue to be developed. Pest-resistant plants can reduce pest population growth, the number of pesticide applications and the environmental impact of pesticides. There remains a great need in the art for plants showing resistance to pest organisms. Another object of the present invention is therefore to provide pest resistant plants showing resistance to pest organisms such as nematodes, insects and fungi.
The present invention provides delivery molecules for facilitating the delivery of a double-stranded ribonucleic acid molecule to a pest organism, as well as various uses of the delivery molecule. The present invention also provides complexes of the delivery molecule and chimeric RNAi molecules, i.e. RNA molecules comprising double stranded RNA for the purpose of RNA interference.
Specifically, in a first aspect the present invention relates to an RNA delivery molecule consisting of a polypeptide sequence comprising (i) at least one RNA-binding domain, (ii) at least one targeting polypeptide able to bind to a cellular endocytosis and/or transcytosis receptor molecule and (iii) optionally at least one peptide linker and/or at least one purification tag.
The advantages of the present invention include: the ease of introducing double-stranded RNA into cells or tissues, the low concentration of RNA which can be used, the stability of double-stranded RNA, and the effectiveness of the inhibition. The present invention allows for the introduction of a double-stranded RNA molecule, such as a small interfering RNA, into a cell of a pest organism with greater ease and efficiency than previously possible using conventional methods known in the art. Accordingly, the RNA delivery molecule of the present invention provides a powerful tool for various agronomic and research applications requiring the delivery of dsRNA into a target pest organism.
In another embodiment, the invention relates to a chimeric RNAi molecule comprising
The invention further also relates to a complex comprising an RNA delivery molecule as defined herein and a chimeric RNAi molecule as defined herein.
The present invention further provides various methods of using an RNA delivery molecule described herein, including methods of facilitating delivery of a double-stranded ribonucleic acid molecule into a pest organism. In a second aspect, the present invention therefore relates to a method for delivering a dsRNA molecule to a pest species, comprising:
The present invention also relates to methods for down-regulating expression of a target gene in a pest species. In an embodiment such method for down-regulating expression of a target gene in a pest species comprises:
In an embodiment, the chimeric RNAi molecule consists of an RNA molecule which comprises double-stranded RNA comprising annealed complementary strands, one of which has a nucleotide sequence which is complementary to at least part of a target nucleotide sequence of the target gene, and which further comprises a nucleotide sequence which binds to the RNA-binding domain of the RNA delivery molecule.
In another embodiment, the invention provides a method for down-regulating expression of a target gene in a pest species which comprises:
Another aspect of the invention relates to methods for producing a transgenic plant that is resistant to a pest species, comprising:
In another embodiment, the invention provides a method for producing a transgenic plant that is resistant to a pest species, comprising:
regenerating a plant from said plant cell.
In yet another aspect the present invention also relates to the use of an RNA delivery molecule according to the present invention for delivery of a dsRNA molecule to a pest species and in particular to a target sequence in a pest species.
In yet another aspect the present invention also relates to the use of an RNA delivery molecule according to the present invention for producing a transgenic plant.
In another aspect the present invention also relates to the use of a complex comprising an RNA delivery molecule as defined herein and a chimeric RNAi molecule as defined herein for down-regulating expression of a target gene in a pest species.
In yet another aspect the present invention further relates to the use of a complex comprising an RNA delivery molecule as defined herein and a chimeric RNAi molecule as defined herein for producing a transgenic plant, and for producing a transgenic plant that is resistant to a pest species.
In another aspect, the present invention further relates to a nucleic acid encoding an RNA delivery molecule of the invention and to a vector comprising said nucleic acid.
In another aspect, the present invention provides a host cell which comprises a nucleic acid encoding an RNA delivery molecule of the invention or a vector comprising said nucleic acid.
In another aspect, the present invention relates to a kit comprising at least one RNA delivery molecule as defined herein.
In another aspect, the invention relates to a composition comprising at least one RNA delivery molecule as defined herein. Preferably, the invention also relates to a composition comprising
Preferably, the composition or kit according to the invention further comprise at least one excipient, e.g. an excipient which is suitable for keeping the RNA delivery molecule or the composition in a stabile condition.
The present invention further relates in another aspect to a transgenic plant resistant to a pest species, an essential derived variety thereof, plant part, plant cell or protoplast thereof obtainable by methods according to the present invention.
The invention also provides a transgenic plant, essentially derived variety thereof, plant part, plant cell or protoplast thereof which comprises a nucleic acid encoding an RNA delivery molecule as defined herein, wherein said nucleic acid is heterologous to the genome of said transgenic plant, or an essentially derived variety thereof, plant part, plant cell or plant protoplast thereof.
The invention also provides a transgenic plant which comprises a vector comprising a nucleic acid encoding an RNA delivery molecule of the invention.
The invention further relates to a plant, essentially derived variety thereof, plant part, plant cell or protoplast thereof wherein the plant, essentially derived variety thereof, plant part, plant cell or protoplast thereof has been transformed with a nucleic acid encoding an RNA delivery molecule as defined herein.
In another aspect, the invention relates to a plant, essentially derived variety thereof, plant part, plant cell or protoplast thereof which co-expresses:
In further embodiments, the present invention relates to progeny or parts or derivatives of plants obtained from a plant or essentially derived variety thereof according to the present invention.
In yet another aspect the present invention also relates to a chimeric RNAi molecule comprising a nucleotide sequence recognized by an RNA-binding protein or RNA-binding domain, and a nucleotide sequence corresponding to a target nucleotide sequence of a target gene of a pest species.
Additional aspects of the present invention will be apparent in view of the detailed description, which follows.
The present invention describes an RNA delivery molecule for facilitating the delivery of double-stranded RNA into a target organism, as well as various uses thereof. Specifically, it has been found that RNA delivery molecule may be bound to a double-stranded ribonucleic acid molecule by means of linkage to an RNA binding domain to form a complex between a protein moiety, e.g. the RNA delivery molecule, and a nucleic acid moiety, e.g. an RNA molecule comprising the double stranded RNA that causes interference. Such RNA delivery molecule greatly facilitates uptake efficiency and allows for the efficient in vivo delivery of dsRNA into cells, or tissues of target pest organisms.
While the present invention is primarily directed to the delivery of a double-stranded ribonucleic acid molecule into a pest organism for the purposes of RNA interference, the RNA delivery molecules described herein may also be used to facilitate the delivery of other non-coding RNAs, such as small temporal RNAs, small nuclear RNAs, small nucleolar RNAs or microRNAs, which may be used in applications other than RNA interference.
In accordance with the present invention, a delivery promoting molecule is used to facilitate the uptake and the correct delivery of double stranded RNA to a suitable target site in a plant-feeding pest organism for the purpose of RNA interference.
The terms “RNA delivery module”, “RNA delivery molecule” and “RNA delivery vehicle” are used herein as synonym and refer to the multidomain or multimodular protein which binds to an RNAi mediating molecule.
The term “RNAi” generally means “RNA interference”.
In one embodiment of the present invention, the RNA delivery molecule consists of a polypeptide sequence which comprises:
The expression “at least one” in the context of the present invention means at least two, at least three, at least four, at least five, at least six, etc. and up to at least 10 or at least 15.
These modules can be swapped spatially. For example, the RNA binding domain can be at the N-terminus of the targeting polypeptide or can be at the C-terminus of the targeting polypeptide. The purification module can be at the N-terminus or at the C-terminus of the RNA delivery molecule. Not all modules need to be present. For example, for protein isolation the fourth module is included whereas for in vivo expression it can be present or absent. The separate modules comprised in the RNA delivery molecule will be discussed into more detail hereunder.
In a specific embodiment the invention relates to an RNA delivery molecule consisting of a polypeptide sequence comprising (i) at least one RNA-binding domain, (ii) at least one targeting polypeptide able to bind to a cellular endocytosis and/or transcytosis receptor molecule and (iii) optionally at least one peptide linker.
More in particular, a first module in the RNA delivery molecule according to the present invention comprises an RNA binding module. This module permits to specifically bind RNA to the RNA delivery molecule. The terms “RNA binding module”, “RNA binding molecule” and “RNA binding protein” are used herein as synonym and refer to a protein or an essential part, or a homologue thereof, which is capable of binding RNA. The RNA binding molecule comprises an “RNA binding domain”. An “RNA binding domain” as used herein may bind double-stranded RNA generically or specifically, single-stranded RNA generically or specifically. The RNA binding molecule may bind dsRNA, ssRNA structure specifically.
The term “essential parts thereof” or “functional part thereof” in this context refers to parts of RNA binding proteins which are capable of binding dsRNA, ssRNA or which recognize and bind a secondary structure in an RNA.
The term “homologue” of an RNA binding protein as used herein refers to a protein which has an amino acid sequence that has at least 30% identity, preferably at least 40%, 50%, 60%, 70%, 80% or 90% identity, most preferably at least 95% identity with a functional portion of the amino acid sequence of an RNA binding protein. It should be understood that instead of % “identity”, also the corresponding % “similarity” can be used to define homologues according to the invention.
The term “functional portion” in the context of the present invention means a portion or fragment of the RNA binding protein comprising the RNA-binding domain.
As used herein, the “% identity and % similarity” are calculated using matcher (EMBOSS, based on Bill Pearson's ‘lalign’ application, version 2.0u4 Feb. 1996). Lalign is based on an algorithm developed by X. Huang and W. Miller (Adv. Appl. Math. (1991) 12:337-357) for the “sim” program, which is a linear-space version of an algorithm described by M. S. Waterman and M. Eggert (J. Mol. Biol. (1987) 197:723-728). A EBLOSUM62 was used as a substitution matrix, and a gap penalty of 14 and an extended penalty of 4 for the alignment.
For the purpose of the present invention, the RNA binding protein or RNA binding domain binds an RNA molecule comprising the double-stranded RNA causing interference in a pest species. The RNA binding domain may bind directly to said double-stranded RNA causing interference, through recognition of and binding to one or more RNA sequences within said double-stranded RNA, or through recognition of and binding to an RNA structure within said double-stranded RNA. Alternatively, the RNA molecule comprising the double-stranded RNA causing interference comprises a further RNA sequence which is recognized by the RNA binding protein or RNA binding domain as being a binding site specific for the said RNA binding protein or domain. Said further RNA sequence may be double-stranded, single-stranded or may comprise an RNA structure which is specifically recognized and bound by the RNA binding protein or RNA binding domain.
It should be noted that each of the RNA binding proteins or RNA binding domains may bind to specific RNA sequences, patterns, recognition sites, RNA structures or the like.
Preferred examples of RNA binding proteins include but are not limited to coliphage HK022 Nun protein, Bacillus subtilis LicT protein, or bacteriophage MS2 coat protein or essential parts, or homologues thereof.
In a preferred embodiment, the RNA binding module comprises the coliphage HK022 Nun protein (Genbank entries: nucleotide sequence: X16093 (whole viral sequence); amino acid sequence: P18683, VNBPHK) or essential parts thereof. The nucleotide and amino acids sequences corresponding to the gene encoding the coliphage HK022 Nun protein are illustrated in
In another preferred embodiment the RNA binding module comprises essential parts (for instance comprising any of SEQ ID Nos 4, 6 or 8) of the coliphage HK022 Nun protein.
Preferred examples hereof comprise but are not limited to;
In yet another preferred embodiment the RNA binding module comprises
In another preferred embodiment the RNA binding module comprises homologues of the coliphage HK022 Nun protein. Therefore, according to a further embodiment, the invention also relates to an RNA delivery molecule as described above, wherein said at least one RNA-binding domain comprises a polypeptide having at least 30% identity, preferably at least 40%, 50%, 60%, 70%, 80% or 90% identity, most preferably at least 95% identity with the coliphage HK022 Nun protein (or with the polypeptide as represented in SEQ ID NO 2). It should be understood that instead of % “identity”, also the corresponding % “similarity” can be used to define homologues according to the invention.
In a preferred example, the N-terminal binding-domain of the bacteriophage HK022 Nun protein (SEQ ID NO 2) and in particular the peptide with sequence SEQ ID NO 8 interacts with the box B RNA sequence (SEQ ID NO 15) and in particular with the 11mer RNA sequence represented in SEQ ID NO 16. (Scharpf et al., Eur. J. Biochem. 267, p2397 (2000), Faber et al., J. Biol. Chem. 276, 34, p32064 (2001)).
In another embodiment, the RNA binding module comprises the Bacillus subtilis LicT protein or essential parts thereof (Genbank/Swissprot/PIR entries: nucleotide sequence: Z28340 (D83026, Z99124 for larger genomic fragments); amino acid sequence: P39805, S47216, BAA11696, CAA82194). The nucleotide and amino acid sequences corresponding to the gene encoding the subtilis LicT protein are illustrated in
In another preferred embodiment the RNA binding module comprises essential parts (for instance comprising SEQ ID NO 12) of the Bacillus subtilis LicT protein. Preferred examples hereof comprise but are not limited to the N-terminal domain of Bacillus subtilis LicT protein comprising amino acids 1 to 56 (SEQ ID NO 12) containing the RNA-binding domain.
In yet another preferred embodiment the RNA binding module comprises
In another preferred embodiment the RNA binding module comprises homologues of the Bacillus subtilis LicT protein. Therefore, according to a further embodiment, the invention also relates to an RNA delivery molecule as described above, wherein said at least one RNA-binding domain comprises a polypeptide having at least 30% identity, preferably at least 40%, 50%, 60%, 70%, 80% or 90% identity, most preferably at least 95% identity with the Bacillus subtilis LicT protein (or with the polypeptide as represented in SEQ ID NO 10), preferably said RNA-binding domain comprises a polypeptide having at least 60% identity, preferably at least 70%, 80% or 90% identity, most preferably at least 95% identity with the RNA binding domain of the Bacillus subtilis LicT protein (i.e. with the polypeptide as represented in SEQ ID NO 12). A non-exhaustive list of such homologous polypeptides is given in Table 1, and may further include representative members of the LicT/SacY family of transcriptional ATs from Bacillus subtilis, Bacillus stearothermophilus, Listeria mnocytogenes, Clostridium longisporum, Clostridium acetobutylicum, Staphylococcus carnosus, Streptococcus agalactiae, Lactococcus lactis, Lactobacillus casei, E. coli and Erwinia chrysanthemi. It should be understood that instead of % “identity”, also the corresponding % “similarity” can be used to define homologues according to the invention.
In a preferred embodiment, the LicT RNA-binding domain (comprising SEQ ID NO 12) interacts with the Bacillus subtilis ribonucleic antiterminator (RAT) that has a secondary structure as depicted in
In yet another preferred embodiment, the RNA binding module comprises the bacteriophage MS2 coat protein or essential parts thereof (Genbank/Swisprot/PIR entries: nucleotide sequence: V00642 (whole genome), NC—001417 (whole genome); amino acid sequence: PO3612, CAA23989, NP—040648, VCBPM2, 721932A).
In another preferred embodiment the RNA binding module comprises essential parts (comprising the RNA binding domain) of the bacteriophage MS2 coat protein. Other preferred examples of suitable RNA binding modules according to the present invention may comprise but are not limited to
In another preferred embodiment the RNA binding module comprises homologues of the bacteriophage MS2 coat protein. Therefore, according to a further embodiment, the invention also relates to an RNA delivery molecule as described above, wherein said at least one RNA-binding domain comprises a polypeptide having at least 30% identity, preferably at least 40%, 50%, 60%, 70%, 80% or 90% identity, most preferably at least 95% identity with the bacteriophage MS2 coat protein (or with the polypeptide as represented in SEQ ID NO 14), preferably said RNA-binding domain comprises a polypeptide having at least 60% identity, preferably at least 70%, 80% or 90% identity, most preferably at least 95% identity with the RNA binding domain of the MS2 coat protein. A non-exhaustive list of such homologous polypeptides is given in Table 2. It should be understood that instead of % “identity”, also the corresponding % “similarity” could be used to define homologues according to the invention.
In a preferred embodiment, the bacteriophage MS2 coat protein (SEQ ID NO 14) interacts with RNA stem-loops that have a secondary structure as depicted in
The present invention thus relates to an RNA delivery molecule as described above, wherein said at least one RNA-binding domain (i) is chosen from:
A second module of the RNA delivery molecule comprises a targeting module. The terms “targeting module”, “targeting molecule”, “targeting protein” and “targeting polypeptide” are used herein as synonym and refer to a protein, or an essential part, or a homologue thereof capable of targeting the RNA delivery molecule to a targeting site in a living pest organism. The term “essential parts thereof” refers to parts of a targeting protein which are capable of targeting the RNA delivery molecule to a targeting site in a living pest organism. The term “homologue” of a targeting protein as used herein refers to a protein which has an amino acid sequence that has at least 30% identity, preferably at least 40%, 50%, 60%, 70%, 80% or 90% identity, most preferably at least 95% identity to a functional portion of the amino acid sequence of a targeting protein. It should be understood that instead of % “identity”, also the corresponding % “similarity” could be used to define homologues according to the invention.
The term “functional portion” in the context of the present invention means a portion or fragment of the targeting protein comprising the domain or sequence which binds to the target cell or tissue in the pest organism.
As used herein the term “targeting site” refers to a specific cell or tissue in a living pest organism, as defined herein, to which the RNA delivery molecule according to the present invention is targeted.
The targeting module preferably comprises a protein which is capable of being endocytosed and/or transcytosed in a cell of the pest organism, or a protein able to bind an endocytosis and/or transcytosis receptor molecule present on a cell or a tissue of the pest organism, or any combinations thereof. In a preferred embodiment, the invention relates to an RNA delivery molecule as described above, wherein said at least one targeting polypeptide binds to a gut cell endocytosis or transcytosis receptor molecule. In another preferred embodiment, the invention relates to an RNA delivery molecule as described above, wherein said at least one targeting polypeptide binds to a tissue cell endocytosis or transcytosis receptor molecule.
“Endocytosis” is defined herein as the cellular uptake of macromolecules and particulate substances by localized regions of the plasma membrane that surround the substance and pinch off to form an intracellular vesicle. “Receptor-mediated endocytosis” is an essential process in all eukaryotes, including invertebrates such as insects or nematodes, and is required for general cellular functions, including uptake of nutrients (e.g., low-density lipoprotein [LDL] or transferrin) and recycling of membranes and membrane proteins.
“Transcytosis” is defined herein as the process by which a molecule may enter through one side of a cell and then migrate across the cell to exit on the other side. Transcytosis refers to the transport of substances across an epithelium by uptake into and release from coated vesicles. Also “receptor-mediated transcytosis” is an essential process in eukaryotes.
In certain embodiments of the present invention, the RNA delivery molecule comprises one targeting molecule, for instance a targeting molecule which allows endocytosis into the gut cell of a pest organism. In another example, the targeting molecule allows transcytosis from the lumen of the gut to the coelumic fluid or haemolymph of the pest organism. In other embodiments of the present invention the RNA delivery molecule comprises one targeting molecule which allows endocytosis into a tissue cell of the pest organism, such as for instance, but not limited to, a muscle cell, a gonade cell, a nerve cell. In another example, the targeting molecule allows transcytosis from an endothelial cell lining an organ to the lumen of said organ of the pest organism. In still other embodiments of the present invention, the RNA delivery molecule comprises two targeting molecules, for instance one targeting molecule which allows transcytosis from the gut cell of a pest organism to the coelumic fluid or haemolymph of the pest organism, and another targeting molecule which allows endocytosis into a tissue cell of the pest organism.
In particular examples, where the pest species is a fungal species, the term “endocytosis” is to be understood in the context of the fungi's feeding process. Upon feeding, fungi secrete enzymes or proteins in the process used by said fungal species for uptake of nutrients. As part of the feeding process, said enzyme or protein (bound or not to nutrients) is taken up again by said fungal species through endocytosis processes. Therefore, according to the present invention, the complex between the RNA delivery molecule and the dsRNA molecule that may cause RNA interference in the fungus, may simultaneously be taken up by the fungus through binding of a domain in the RNA delivery molecule to a secreted enzyme or protein (or to a part thereof, which is re-uptaken). The present invention is thus equally applicable to target the RNA delivery molecule or the complex to endocytosed proteins (or to their receptors on the fungal cell wall) in fungi.
In another embodiment, the targeting molecule comprises at least one sequence which is recognized by a gut cell or a receptor on the gut cell of a pest organism, and which recognition triggers the endocytosis or transcytosis of the complex between the RNA delivery molecule and the chimeric RNAi molecule.
Preferred examples of endocytosis receptor binding molecules suitable for use in the present invention comprise but are not limited to
In a preferred embodiment, the endocytosis receptor binding molecule suitable for use in the present invention comprises transferrin proteins from any pest species, such as nematode or insect species, lectins such as snowdrop lectin, and coat proteins from viruses such as Luteoviridae.
Preferred examples of transcytosis receptor binding molecules suitable for use in the present invention comprise but are not limited to:
In another preferred embodiment, the transcytosis receptor binding molecule suitable for use in the present invention comprise lectins such as snowdrop lectin, and coat proteins from viruses such as Luteoviridae.
In the examples section, a non-limiting number of RNA delivery molecules are described, comprising targeting polypeptides according to the invention.
According to yet another aspect of the invention, the RNA delivery molecule does not comprise a targeting polypeptide. The RNA delivery molecules according to this aspect of the invention may further comprise all elements of RNA delivery molecules as described herein. The major advantage of these RNA delivery molecules is that it may protect RNAi molecules by binding them in the complex, i.e. protection from plant Dicer and/or other plant degradation systems. Another advantage is that the RNA delivery molecule may direct and/or store the chimeric RNAi molecule of the invention in plant organelles, for instance in case the chimeric RNAi molecules do not encode such signals.
The RNA delivery module according to the invention preferably comprises a third module which consists of at least one peptide linker for linking the first to the second module. Said linker polypeptide preferably comprises a polypeptide of at least 3, preferably at least 4 or 5, most preferably at least 7, and more preferably at least 12 amino acids. Preferably said linker is a polypeptide comprising between 3 and 15 amino acids. Preferably said linker is a polypeptide comprising non-charged amino acids such as glycine, serine, cysteine, asparagine, tyrosine, glutamine, alanine, valine, proline, threonine, and preferably glycine or serine. A preferred example of a linker polypeptide comprises the polypeptide having the amino acid sequence GGGGSGGGGSGGGGS (SEQ ID NO 53). In preferred examples, the linker polypeptide comprises one of the following:
In a preferred embodiment, the present invention thus relates to an RNA delivery molecule as described above further comprising at least one linker module, preferably a linker module as described above.
The RNA delivery module according to the invention may further comprise a fourth module which consists of a purification tag. Said purification tags, defined by specific amino acid sequences, enables the easy purification of the tagged delivery molecule. Preferred examples of purification modules comprise but are not limited to His-tag, GST-tag, c-myc-tag, FLAG-tag, E-tag.
The invention thus further relates to an RNA delivery molecule as described above, further comprising a purification tag, preferably a purification tag as described above.
The term “chimeric RNAi molecule” or “RNAi molecule” as used herein means a sequence that contains
In the context of the present invention, the sequence corresponding to the target nucleotide sequence is contained in a double-stranded RNA (dsRNA) wherein said double-stranded RNA comprises annealed complementary strands, one of which has a nucleotide sequence which is complementary to at least part of a target nucleotide sequence of a target gene. The expressions “chimeric RNAi molecule”, “RNAi mediating molecule”, and “chimeric RNAi mediating molecule” all relate to a sequence containing a sequence corresponding to a target nucleotide sequence and the RNA sequence recognized by the RNA-binding protein or RNA-binding domain.
Preferred examples of chimeric RNAi molecules are molecules that consist of a target RNA sequence and an RNA sequence that is recognized by an RNA binding module as described in the present invention. The RNA sequences that are recognized by an RNA binding protein or RNA binding domain include but are not limited to RNA sequences recognized by the coliphage HK022 Nun protein, Bacillus subtilis LicT protein, or bacteriophage MS2 coat protein or essential parts, or homologues of said RNA binding proteins. The RNA sequences that are recognized by an RNA binding module as described in the present invention are specific, meaning that RNA sequences identical or comprising the consensus sequences as depicted in
In a preferred embodiment, the present invention relates to a chimeric RNAi molecule comprising
Table 3 provides an overview of different RNA sequences contained in chimeric RNAi molecules according to the present invention which are specifically recognized by a Nun, LicT or MS2 RNA-binding protein or RNA-binding domain as indicated.
According to a preferred embodiment, said chimeric RNAi molecule is a molecule as described in Example 2. According to further embodiments, the chimeric RNAi molecule has a sequence as represented in any of
In yet another embodiment, the present invention relates to a chimeric RNAi molecule according to the present invention as represented by any of SEQ ID NOs 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 55 or 56. In another embodiment, the present invention relates to a chimeric RNAi molecule according to the present invention as represented by any of SEQ ID NOs 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71. In yet another embodiment, the present invention relates to a chimeric RNAi molecule according to the present invention as represented by any of SEQ ID NOs 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86.
Table 4 provides an overview of different examples of chimeric RNAi molecules according to the present invention which contain an RNA sequence that is specifically recognized by a Nun, LicT or MS2 RNA-binding protein or RNA-binding domain or essential parts, or homologues thereof as indicated.
In another embodiment, the present invention relates to the use of a chimeric RNAi molecule as defined herein, and in particular as represented by any of SEQ ID NOs 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85 or 86 for down-regulation of target genes in a pest species, for delivering dsRNA and/or for producing transgenic plants resistant to pest organisms.
A “target gene” as used herein means a gene that needs to be silenced in the target (pest) species. The target gene may be selected from the genome of any species as described herein. According to a preferred embodiment, the target sequence is chosen from the genome of an organism which organism is different from the organism in which the dsRNA capable of causing interference is expressed. This means that the dsRNA is expressed in one (host) cell or organism and is subsequently transferred (or taken up by) to another cell or organism comprising the target gene. According to one specific embodiment of the present invention, the dsRNA is expressed in the plant or a plant cell and the target gene is chosen from the genome of a bacterium, a virus or an invertebrate, more particularly from a plant pest species such as a nematode, fungus or an insect. In the present context, the expression “dsRNA” relates to double stranded RNA capable of causing RNA interference. In another embodiment, the dsRNA is expressed in a bacterial or fungal cell and the bacterial or fungal cell is taken up or eaten by the pest species. According to still another embodiment, the dsRNA is isolated from, or purified from, the bacterial or fungal cell expressing the dsRNA, and the dsRNA is provided as a pesticide or in a pesticidal formulation to the pest species.
Particular suitable target genes are genes that are involved in an essential biological pathway of the target pest species, meaning that the target gene is an essential gene to the target pest species and that gene silencing of the target gene has an adverse effect on the viability the growth, development, feeding, movement, and/or reproduction of the target pest species. Suitable target genes are genes associated with infection, propagation or pathogenesis of the pest species in the host. In another preferred embodiment the sequence of the target RNA in the pest organism comprises sequences of genes which are essential for development, neural function, reproduction or digestion of the pest organism.
In accordance with the present invention, any suitable double-stranded RNA fragment capable of directing RNAi or RNA-mediated gene silencing of a target gene can be used.
As used herein, a “double-stranded ribonucleic acid molecule (dsRNA)” refers to any RNA molecule, fragment or segment containing two strands forming an RNA duplex, notwithstanding the presence of single stranded overhangs of unpaired nucleotides.
The double-stranded RNA comprises annealed complementary strands, one of which has a nucleotide sequence which corresponds to a target nucleotide sequence of the target gene to be down-regulated. The other strand of the double-stranded RNA is complementary to this target nucleotide sequence.
According to the invention, the “dsRNA” or “double stranded RNA”, whenever said expression relates to RNA that is capable of causing interference, may be formed from two or more separate polynucleotide strands which together form a double stranded, folded or assembled structure which includes at least one double-stranded portion effective in gene silencing by RNAi. For example, said dsRNA may be formed form two separate (sense and antisense) RNA strands that are annealed together. In this embodiment, the sense and antisense strands of the dsRNA originate form distinct RNA molecules, wherein at least one of the RNA molecules is a chimeric RNAi molecule as described above, expressed in the same or in another cell, and which RNA molecule may or may not comprise other domains or sequences which protect it from degradation or which direct it to specific locations. The RNA molecules may, when folded or assembled, include both double-stranded and single-stranded regions. The dsRNA may also comprise other sequences that are not complementary to a target gene or sequence but that have other functions.
Alternatively, the dsRNA may be formed from a single RNA polynucleotide molecule which includes regions of self-complementarity, such that when folded it is capable of forming a structure including one or more double-stranded portions (also referred as “dsRNA fragment(s)”) effective in gene silencing by RNAi. For example, the dsRNA may have a foldback stem-loop or hairpin structure wherein the two annealed strands of the dsRNA are covalently linked. In this embodiment, the sense and antisense strands of the dsRNA are formed from different regions of a single chimeric RNAi molecule that is partially self-complementary. The features of “hairpin” or “stem-loop” RNAs for use in RNAi are generally known in the art (references: WO 99/53050). The organization of sense and antisense portions making up the double stranded RNA is variable. RNAs having this structure are convenient if the dsRNA is to be synthesized by expression in vivo, for example in a host cell or organism as discussed below, or by in vitro transcription. Non-limiting examples of the organization of sequences within a chimeric RNAi molecule are represented in
Further, as used herein, a double-stranded ribonucleic acid molecule may further include single stranded RNA molecules forming functional stem-loop structures, such as small temporal RNAs, short hairpin RNAs and microRNAs, thereby forming the structural equivalent of an RNA duplex with single strand overhangs. The RNA molecule of the present invention may be isolated, purified, native or recombinant, and may be modified by the addition, deletion, substitution and/or alteration of one or more nucleotides, including non-naturally occurring nucleotides, including those added at 5′ and/or 3′ ends to increase nuclease resistance.
If the methods of the invention are to be used for controlling growth or infestation of a pest organism in a host, it is preferred that that the dsRNA is not harmful for organisms other than the target organism(s), and consequently the double-stranded RNA does not share any significant homology with any host gene, or at least with any essential gene of the host. In this context, it is preferred that the double-stranded RNA shows less than 30%, more preferably less that 20%, more preferably less than 10%, and even more preferably less than 5% nucleic acid sequence identity with any gene of the host cell. % sequence identity should be calculated across the full length of the double-stranded RNA sequence capable of causing RNA interference. If genomic sequence data is available for the host organism then it is simple to cross-check sequence identity with the double-stranded RNA using standard bioinformatics tools.
Alternatively, in this context, it is preferred that 21 contiguous base pairs of the dsRNA do not occur in the genome of the host organism.
Preferably, the double-stranded RNA sequence capable of causing RNA interference does not have 20 contiguous nucleotides in common with a sequence of an organism other than the target organism. For example, when the target organism is a plant pathogen, such as a plant parasitic nematode or an insect, the double-stranded RNA does not have 20 contiguous nucleotides in common with a nucleotide sequence from a plant or a mammal (a human in particular).
The “target region” of the target pest gene may be any suitable region of the gene. The target region should comprise at least 17 or 18 consecutive nucleotides of the target gene, more preferably at least 19, 20 or 21 nucleotide and still more preferably at least 22, 23, 24 or 25 nucleotides of the target gene.
The term “complementarity” as used herein relates to DNA-DNA and RNA-RNA complementarity as well as to DNA-RNA complementarity. In analogy herewith, the term “RNA equivalent” means that in a DNA sequence(s), the base “T” may be replaced by the corresponding base “U” normally present in ribonucleic acids.
The term “nucleotide sequence which is complementary to” means a sequence that is complementary to at least part of a nucleotide sequence of a target gene. The term “complementary” when used in the context of the present invention for a dsRNA, means having substantial sequence identity to one of the strands of the target gene. In the present invention, the complementary sequence will generally comprise a nucleotide sequence having more than about 75% sequence identity to the corresponding sequence of the target gene, however, a higher homology might produce a more efficient inhibition of expression of the target gene. Preferably, the sequence identity is about 80%, 85%, 90%, 95%, and even more preferably more than about 99%. In the context of the present invention, the expression “more than about” has the same meaning as “at least”.
It is most preferred that (at least part of) the double-stranded RNA will share 100% sequence identity with the target region of the target pest gene. However, it will be appreciated that 100% sequence identity is not essential for functional RNA inhibition. RNA sequences with insertions, deletions, and single point mutations relative to the target sequence have also been found to be effective for RNA inhibition. The term “corresponding to”, when used to refer to sequence correspondence between the double-stranded RNA and the target region of the target gene, is therefore to be interpreted accordingly as not absolutely requiring 100% sequence identity.
Although the dsRNA must contain a sequence which corresponds to the target region of the target gene (i.e. wherein one strand of the dsRNA is complementary to at least part of a target (e.g. pest) nucleotide sequence) it is not absolutely essential for the whole of the dsRNA to correspond to the sequence of the target region. For example, the dsRNA may contain short non-target regions flanking the target-specific sequence, provided that such sequences do not affect performance of the dsRNA in RNA inhibition to a material extent.
In another embodiment, the dsRNA may comprises multiple dsRNA fragments, each fragment comprising annealed complementary strands, one of which is complementary to a least part of a target nucleotide sequence to be silenced. Multiple dsRNA fragments as used in the present invention are also generally referred as to “concatemers”. Thus, the present invention provides a chimeric RNAi molecule comprising:
The term “multiple” in the context of the present invention means at least two, at least three, at least four, at least five, at least six, etc. and up to at least 10, 15, 20 or at least 30.
Non-limiting examples of suitable concatemers for use in the present invention include concatemer cloverleaf, concatemer dumbbell, concatemer hairpin, concatemer stem dsRNA.
In one embodiment, said dsRNA comprises multiple dsRNA fragments that are complementary to different (e.g. distinct) sequences in one target gene. In another embodiment, said dsRNA comprises multiple dsRNA fragments that are complementary to different (e.g. distinct) target genes. In yet another embodiment, said dsRNA comprises at least one repeat of one dsRNA fragment. As used herein “one repeat” means two copies of the same dsRNA fragment. In yet another embodiment, said dsRNA comprises at least two or three copies, preferably at least four, five or six copies, more preferably at least seven, eight, nine ten or more copies of one (e.g. the same) dsRNA fragment. In other words, said multiple dsRNA fragments are repeats of a single dsRNA fragment. In one preferred embodiment, the dsRNA fragments are not separated by non-hybridizing RNA fragments. In another embodiment, the dsRNA fragments are separated by a linker or spacer sequence. Preferably, the linker or spacer sequence is double stranded and the strands are complementary, thus also forming a double stranded region. The linker sequence may comprise a short random nucleotide sequence that is not complementary to target sequences. In another embodiment, the dsRNA fragments are not separated by a linker, a spacer or a lock sequence as described further.
The present invention encompasses chimeric RNAi molecules comprising at least one nucleotide sequence recognized by an RNA-binding protein or RNA-binding domain, and one dsRNA fragment comprising annealed complementary strands, one of which has a nucleotide sequence which is complementary to a least part of a target nucleotide sequence of a pest target gene, and which comprises one or more additional dsRNA fragments, each comprised of annealed complementary strands, wherein at least one complementary strands of each dsRNA fragment, comprises each independently a nucleotide sequence which is complementary to
It should be clear that the expression “multiple dsRNA” in the chimeric RNAi molecule also encompasses chimeric RNAi molecules comprising copies of one or more dsRNA fragments and further comprising other dsRNA fragments, that are different from the repeated or copied dsRNA fragments. Therefore, the invention also relates to chimeric RNAi molecule comprising in addition to at least one nucleotide sequence recognized by an RNA-binding protein or RNA-binding domain, one or more repeats of dsRNA fragments and further comprising at least one dsRNA fragment which is distinct from the repeated fragment(s).
In the concatemer comprising chimeric RNAi molecule, the length of each of the dsRNA fragments may be at least 17 bp, 18 bp, 19 bp, 20 bp, 21 bp, 22 bp, 23 bp, 24 bp, 25 bp or more, for example about 30 bp, about 40 bp, about 50 bp, about 60 bp, about 70 bp, about 80 bp, about 90 bp, about 100 bp, about 110 bp or about 120 bp. Preferred dsRNA fragments in a concatemer comprising chimeric RNAi molecule have a length between 17 and 300 bp, preferably between 21 and 250 bp, preferably between 40 and 150 bp, more preferably between 50 and 120 bp or any number in between.
The terms “another target gene” or “a further target gene” are use interchangeably and mean for instance a second, a third or a fourth, etc. target gene.
According to one preferred embodiment, the dsRNA fragments target at least one target gene that is essential for viability, growth, development or reproduction of the pest and target at least one gene involved in pathogenicity or infectivity. Alternatively, the dsRNA fragments target multiple genes of the same category, for example, the dsRNA fragments target at least two essential genes or at least two genes involved in pathogenicity or at least two genes involved in any of the cellular functions. According to a further embodiment, the dsRNA fragments target at least two target genes, which target genes are involved in a different cellular function. For example, the dsRNA fragments target two or more genes involved in protein synthesis (e.g. ribosome subunits), protein degradation (e.g. proteasome subunits), formation of microtubule cytoskeleton (e.g. beta-tubulin gene), and the like.
The dsRNA fragments in the chimeric RNAi molecule may be combined as follows:
The present invention thus encompasses a chimeric RNAi molecule comprising at least one nucleotide sequence recognized by an RNA-binding protein or RNA-binding domain and multiple dsRNA fragments targeting different target genes which originates from a single target (or pest) species, or wherein said different target genes originates from distinct target (or pest) species, for instance pest species belonging to the same (in one embodiment) or to different (in other embodiments) genera, families, orders or even phyla.
The chimeric RNAi molecules comprising such multiple dsRNA fragments and targeting multiple target genes, are characterized by stacking multiple RNAi capacity, resulting in synergetic effects, and capable of triggering multiple RNAi effects in the target cell or target organism.
The dsRNA may further contain DNA bases, non natural bases or non-natural backbone linkages or modifications of the sugar-phosphate backbone, for example to enhance stability during storage or enhance resistance to degradation by nucleases.
The double-stranded RNA fragment capable of causing interference will itself preferably be greater than 17 bp in length, preferably 19 bp in length, more preferably greater than 20 bp, more preferably greater than 21 bp, or greater than 22 bp, or greater than 23 bp, or greater than 24 bp, or greater than 25 bp in length.
The design and production of suitable chimeric RNAi molecules comprising double stranded RNA for the present invention is documented in the examples section. Optionally, within the chimeric RNAi molecules of the present invention, there may be included one or more moieties capable of protecting the double stranded RNA portion (causing RNA interference) against RNA processing. Such moieties and constructs are described in a patent application of applicant having application number 0423659.2 and which was filed on Oct. 25, 2004 at the UK Patent Office (and of which the publication number will be provided once available) and other patent applications of applicant having application number U.S. 60/621,800 and which was filed on Oct. 25, 2004 and having application number U.S. 60/683,551 which was filed on May 5, 2005, at the US Patent and Trademark Office (and of which the publication number will be provided once available). Both patent applications are incorporated herein in their entirety. Chimeric RNAi constructs according to the present invention may thus comprise different dsRNA core types, optionally comprising linker types, optionally comprising different lock types designed to protect the dsRNA core against RNA processing in the host cell expressing the dsRNA construct. In one embodiment of the invention a sequence capable of protecting the dsRNA against RNA processing is also referred to as a “lock”. (For the terminology used in this particular section, relating to protection of dsRNA, reference is made to the above-mentioned UK and US patent applications by applicant).
Whenever a stabilized or protected chimeric RNAi molecule is described, the term “core” refers to the dsRNA portion, which core may comprise at least one dsRNA fragment or which may comprise multiple dsRNA fragments.
The term “dsRNA core” as used herein refers to the core of the dsRNA molecule. Different dsRNA core types are for example a single stem comprising one dsRNA, a single stem comprising multiple dsRNA fragments (concatemer) which dsRNA fragments are each independently complementary to one target gene or to different target sequences of one target gene or are complementary to different target genes.
The term “lock” as used herein refers to a sequence capable of protecting the dsRNA or a portion thereof against RNA processing. Different lock types include a GC rich clamp, a short loop of about 4 or of about 5 base pairs, a mismatch lock, or a protein binding RNA structure such as an IRES, a 5′ region of a virus, an Iron responsive element or other RNA motifs that are recognized by proteins.
Other mechanisms to protect the dsRNA against RNA processing may be combined within the chimeric RNAi molecules of the present invention, for example embedding the dsRNA in viroids or in natural unprocessed RNA structures (such as mi RNA, tRNA, ribosomal RNA, components of the spliceosome or other non-coding RNA's transcribed from RNA polymerase I, II or III promoters). Embedding the dsRNA in a viroid-like dsRNA structure is described and illustrated for instance in Navarro and Flores (2000 EMBO Journal 19(11) p 2662. The dsRNA may be incorporated within the viroid as such, or in the viroid mutated to avoid internal cleavage (for example by ribozymes) or to avoid translation. Mutations can be based on information from Dais et al. (1991, NAR 19(8), p 1893). These type of constructs may be transported to the chloroplasts, where it can receive extra protection against dsRNA processing.
Another mechanism to protect dsRNA from processing is to signal the dsRNA towards an intracellular compartment of the host cell. For example, the dsRNA can be compartmentalized in an intermediate host cell, before it is transferred to the target host cell. In particular, the chimeric RNAi molecule may be compartmentalized in a plant cell, for example, it may be located in the chloroplast, mitochondrion or plastid, before it is transferred to the plant pest species, for example the plant pest nematode or insect. Compartmentalization may occur in a variety of ways, such as for example via the use of viroid structures, or via the use of signal sequences, for example chloroplast, mitochondrial or plastid signal sequences. These organelles are from prokaryotic origin and may offer a protective environment away from the plant RNA processing machinery.
The term “linker” as used herein for the chimeric RNAi molecule refers to a molecule enabling linking of a lock to a dsRNA core. Different linker types are conditionally self-cleaving RNA moieties such as linkers that are cleaved at low pH or at high pH or that are cleaved in hydrophobic conditions, or are one of an intron, or a non-complementary RNA sequence. Optionally, the chimeric RNAi molecule may comprise an interstem base pairing moiety or can be in the form of a triple RNA. In a preferred embodiment, the multiple dsRNA fragments of the chimeric RNAi molecule are connected without linker. In another embodiment, a linker is present between the at least one nucleotide sequence recognized by an RNA-binding protein or RNA binding domain and the dsRNA in the chimeric RNAi molecule. In still another embodiment, the multiple dsRNA fragments of the chimeric RNAi molecule are connected by one or more linkers.
In a particular embodiment, the linkers may be used to disconnect smaller dsRNA regions in the pest organism. Advantageously, in this situation the linker sequence may promote division of a long dsRNA into smaller dsRNA under particular circumstances, resulting in the release of separate dsRNA fragments under these circumstances and leading to more efficient gene silencing by these smaller dsRNA fragments. Non-limiting examples of suitable conditionally self-cleaving linkers are RNA sequences that are self-cleaving at suitable pH conditions. Suitable examples of such RNA sequences are described by Borda et al. (Nucleic Acids Res. 2003 May 15, 31(10):2595-600), which document is incorporated herein by reference. This sequence originates form the catalytic core of the hammerhead ribyozome HH16. Alternatively, the linkers are self cleaving in the endosomes. This may be advantageous when the chimeric RNAi molecule of the invention is taken up by the pest via endocytosis or transcytosis, and are therefore compartmentalized in the endosomes of the pest. The endosomes may have a low pH environment, leading to the cleavage of the linker. Linkers that are self-cleaving in hydrophobic conditions are particularly useful in chimeric RNAi molecules of the present invention when used to be transferred from one cell to another via the transit in a cell wall, for example when crossing the cell wall of a pest. Particular plant pest organisms of interest for application of this technique are plant parasitic fungi or plant parasitic viruses or bacteria.
An intro may be used as a linker. An “intron” as used herein may be any non-coding RNA sequence of a messenger RNA. Particular suitable intron sequences for the chimeric RNAi molecules of the present invention are (1) U-rich (35-45%); (2) have an average length of 100 bp (varying between about 50 and about 500 bp) which base pairs may be randomly chosen or may be based on known intron sequences; (3) strat at the 5′ end with -AT:GT- or -CG:GT- and/or (4) have at their 3′ end -AG/GC- or AG:AA.
According to the invention, a linker sequence may be present between the dsRNA fragments or not. Preferably, no linker sequence is present between the dsRNA fragments. For instance when the dsRNA comprising the dsRNA fragments is chemically synthesized, the dsRNA fragments may be directly adjacent to each other, without the presence of non-target sequences. When present, the linker may for instance comprise a short random nucleotide sequence that is not complementary to target sequences but that is the result of the cloning.
A by itself non-complementary RNA sequence, ranging from about 1 base pair to about 10000 base pairs, for instance of at least 10, 20, 30, 50, 60, 70, 80, 90, 100, 200, 500, 1000, 1500, 2000, 3000, 10000 base pairs, or any number in-between, may also be used as a linker.
The choice of target gene(s) to be targeted by a chimeric RNA molecule depends on the choice of target gene which is to be silenced in the target organism or organisms in order to achieve the desired effect of pest control. For the chimeric RNA molecule designed herein below the target gene(s) was (were) chosen from one or more of the following categories of genes:
The RNA delivery molecules, chimeric RNAi molecules, complexes thereof and methods of the present invention are particularly useful to target multiple sequences simultaneously. These multiple sequences may originate from one target gene. Alternatively, the multiple target sequences may originate from multiple target genes. These multiple target genes may originate from one and the same pest species. Alternatively, these multiple target genes may originate from different pest species from the same or different order. Therefore, one chimeric RNAi molecule of the present invention, for example in the form of a concatemer cloverleaf, a concatemer stem, or a concatemer hairpin, may simultaneously target multiple sequences originating from the same and for multiple target genes of the same and or different pest species, such as from nematodes, insects, bacteria and/or fungi.
According to one particular embodiment of the present invention, the RNA delivery molecules, chimeric RNAi molecules, or complexes thereof targets multiple target genes originating from multiple species. For example, a chimeric RNAi molecule may target multiple genes from multiple plant pest organisms, and by expressing the chimeric RNAi molecule in the plant, the plant acquires resistance against multiple plant pests simultaneously. Similarly, a plant or a surface or substance susceptible to pest infestation may be sprayed with a composition (or the like) comprising the RNA delivery molecules, chimeric RNAi molecules, or complexes thereof, thereby protecting the plant or the surface or substance against infestation from multiple pests. For example, the plant acquires resistance against nematodes and insects, or against nematodes, insects and/or fungi. Also the chimeric RNAi molecule allows the plant to acquire resistance against multiple nematodes of a different genus, family, order or class, and/or against insects of a different genus, family or order, and/or against fungi of a different genus, family or order.
In another particular embodiment of the present invention, the chimeric RNAi molecule targets multiple target genes originating from different species from the same order. For example, one chimeric RNAi molecule which targets genes of different bacterial, viral, fungal, insect or nematode species, may be used as an effective and broad spectrum bacteria, virus, fungus, insect killer or broad spectrum nematode killer. Combination of dsRNA fragments with at least one nucleotide sequence recognized by an RNA-binding protein or RNA-binding domain into one chimeric RNAi molecule according to the present invention, wherein said dsRNA fragments are targeting multiple target sequences from different pest species is favorable to enlarge the pest species spectrum of the RNAi effect of the dsRNA molecules.
In another particular embodiment of the present invention, the chimeric RNAi molecule targets multiple target genes originating from the same organism, for example from the same pest species. Such a construct offers the advantage that several weak target genes from the same organism can be silenced together to efficiently control the pest organism, while silencing one or more of the weak target genes separately is not effective to control the pest. Also, several strong target genes from the same organism can be silenced simultaneously, in order to further improve the efficacy of the pest control, or to avoid the occurrence of resistance of the pest organisms by mutation.
The terms “target organism” or “target species” or “pest organism” or “pest species” are used herein as synonym and refer to any organism or species which needs to be killed or paralyzed. Suitable target species are chosen from the group comprising fungi, insects, mites, protozoa, metazoa (comprising nematodes), algae, plants, animals (including mammals). Most suitable for the methods of the present invention are target species which are pest organisms. Preferably, in the context of the present invention, the term “target species” or “pest species” refers to plant pest organisms such as nematodes, insects and fungi and preferably refers to any organism classified in the taxonomical group of the Insecta or of the Nematoda, or of the Fungi.
“Nematodes” as used herein comprises species of the order Nematoda. Many species of nematodes are parasitic and cause health problems to humans and animals (for example species of the orders Ascaradida, Oxyurida, Strongylida, Stronglyloides and Trichocephalida), as well as to plants and fungi (for example species of the orders Aphelenchida, Tylenchida ad others). Preferably, “nematodes” as used herein refers to plant parasitic nematodes and nematodes living in the soil. Plant parasitic nematodes include, but are not limited to, ectoparasites such as Xiphinema spp., Longidorus spp., and Trichodorus spp.; semiparasites such as Tylenchulus spp.; migratory endoparasites such as Pratylenchus spp., Radopholus spp., and Scutellonerna. spp.; sedentary parasites such as Heterodera spp., Globodera spp., and Meloidogyne spp., and stem and leaf endoparasites such as Ditylenchus spp., Aphelenchoides spp., and Hirshmaniella spp. According to a preferred embodiment of the invention, the nematodes are plant parasitic nematodes, in particular root parasitic soil nematodes such as, for example, those of the genera Heterodera and Globodera (cyst-forming nematodes) and Meloidogyne (root knot nematodes). The RNA constructs of the present invention are particularly suitable to control harmful species of the genus Meloidogyne, such as for example, Meloidogyne incognita, and of the genus Heterodera, such as for example, Heterodera glycines (soybean cyst nematode) and also of the genus Globodera, such, as for example, Globodera rostochiensis (potato cyst nematode) and also representatives of migrating endoparasites, such as, for example, Pratylenchus penetrans or Radopholus similes and representatives of ectoparasites, such as, for example, Trichodorus spp. and Xiphinema spp. However, the use of the RNA constructs according to the invention is in no way restricted to these genera, but also extends in the same manner to other nematodes.
“Fungi” as used herein comprises all species of the order Fungi. According to a preferred embodiment of the invention, the target gene originates from a plant parasitic fungus such as Magnaporthe oryzae (rice blast, formerly Magnaporthe grisae; anamorph Pyricularia oryzae Cav. and Pyricularia grisae); Rhizoctonia spp., particularly Rhizoctonia solani and Rhizoctonia oryzae; Gibberella fujikuroi; Sclerotinium spp.; Helminthosporium sigmoideum; Pythium spp.; Alternaria spp., particularly Alternaria solani; Fusarium spp., particularly Fusarium solani and Fusarium germinearum; Acremoniella spp.; Leptosphaeria salvinii; Puccinia spp., particularly Puccinia recondita and Puccinia striiformis; Septoria nodorum; Pyrenophora teres; Rhincosporium secalis; Erysiphe spp., particularly Erysiphe graminis; Cladosporium spp.; Pyrenophora spp.; Tilletia spp.; Phytophthora spp., particularly Phytophthora infestans; Plasmopara viticola; Uncinula necator, Botrytis cinerea; Guiguardia bidwellii; C. viticola; Venturia inaequafis; Erwinia armylovora; Podosphaera leucotricha; Venturia pirina; Phakospora sp (soybean rust), Ustilago maydis (corn smut).
“Insects” as used herein comprises all insect species. In an embodiment said insect species comprise species of the order Lepidoptera. According to a preferred embodiment of the invention, the insects are insects that damage plants, comprising amongst others Leptidopteran insect pests, such as Heliothis spp., Helicoverpa spp., Spodoptera spp., Ostrinia spp., Pectinophora spp, Agrotis spp., Scirphophaga spp., Cnaphalocrocis spp., Sesamia spp, Chilo spp., Anticarsia spp., Pseudoplusia spp., Epinotia spp., and Rachiplusia spp., preferably Heliothis virescens, Helicoverpa zea, Helicoverpa armigera, Helicoverpa punctera, Ostrinia nubilafis, Spodoptera frugiperda, Agrotis ipsilon, Pectinophora gossypiella, Scirphophaga incertulas, Cnaphalocrocis medinalis, Sesamia inferens, Chilo partellus, Anticarsia gemmatalis, Pseudoplusia includens, Epinotia aporema and Rachiplusia nu. e.g. Examples of preferred Insecta include, but are not limited to, members of the orders Coleoptera (Anobium, Ceutorhynchus, Rhynchophorus, Cospopolites, Lissorhopterus spp., Lissorhopterus oryzophilus, Meligethes, Echinocnemus squamos, Hypothenemus, Hylesinus, Acalymma, Lema, Psylliodes, Leptinotarsa, Gonocephalum, Agriotes, Dermolepida, Heteronychus, Phaedon, Tribolium, Sitophilus spp., Sitophilus zeamais, Diabrotica spp. (Diabrotica virgifera virgifera, Daibrotica undecimpunctata howardi, Diabrotica barbell), Oulema oryzae, Chaetocnema pulicaria, Epilachna varivestis, Cerotoma trifurcata, Leptinotarsa decemlineata, Anthonomus spp., Anthonomus grandis, or Anthrenus spp.), Lepidoptera (e.g. Ephestia, Mamestra, Earias, Pectinophora, Ostrinia, Trichoplusia, Pieris, Laphygma, Agrotis, Amathes, Wiseana, Tryporyza, Diatraea, Sporganothis, Cydia, Archips, Plutella, Chilo, Heliothis, Helicoverpa (especially Helicoverpa armigera), Spodoptera or Tineola ssp.), Diptera (e.g. Musca, Aedes, Anopheles, Culex, Glossina, Simulium, Stomoxys, Haematobia, Tabanus, Hydrotaea, Lucilia, Chrysomia, Callitroga, Dermatobia, Gasterophilus, Hypoderma, Hylemyia, Atherigona, Chlorops, Phytomyza, Ceratitis, Liriomyza, and Melophagus spp.), Phthiraptera, Hemiptera (e.g. Laodelphax striatellus, Sogatella furcifera, Rhopalosiphum maidis, Macrosiphum euphorbiae, Aphis spp. (Aphis gossypii, Aphis glycines), Bemisia spp., Bemisia tabaci, Phorodon, Aeneoplamia, Empoasca spp. (Empoasca fabae, Empoasca solana), Parkinsiella, Pyrilla, Aonidiella, Coccus, Pseudococcus, Helopeltis, Lygus, Dysdercus, Oxycarenus, Nezara, Aleurodes, Triatoma, Rhodnius, Psylla, Myzus spp., Myzus persicae, Megoura, Phylloxera, Adelyes, Nilaparvata spp., Nilaparvata lugens, Nephrotettix spp., Nephotettix virescens, or Cimex spp.), Orthoptera (e.g. Locusta, Gtyllus, Schistocerca or Acheta spp.), Dictyoptera (e.g. Blattella, Periplaneta or Blatta spp.), Hymenoptera (e.g. Athalia, Cephus, Atta, Lasius, Solenopsis or Monomorium spp.), Isoptera (e.g. Odontotermes and Reticulitermes spp.), Siphonaptera (e.g. Ctenocephalides or Pulex spp.), Thysanura (e.g. Lepisma spp.), Dermaptera (e.g. Forficula spp.) and Psocoptera (e.g. Peripsocus spp.) and Thysanoptera (e.g. Thrips tabaci).
“Bacteria” that damage plants and that can be controlled with the constructs and methods of the present invention are for example Agrobacterium ssp.; Arachnia ssp.; Clavibacter ssp.; Corynebacterium ssp.; Erwinia ssp.; Fusobacterium ssp.; Hafnia ssp.; Pseudomonas ssp.; Spiroplasma ssp.; Streptomyces ssp.; Xanthomonas ssp.; Xylella ssp. and Xylophilus ssp.
“Viruses” that damage plants and that can be controlled with the constructs and methods of the present invention are for example African cassava mosaic virus; Alfalfa mosaic virus; American plum line pattern virus; Andean potato latent virus; Andean potato mottle virus; Apple chlorotic leaf spot virus; Apple mosaic virus; Apple stem grooving virus; Arabis mosaic virus; Arracacha virus B, oca strain; Asparagus virus 2; Australian grapevine viroid; Avocado sunblotch viroid; Barley mild mosaic virus; Barley stripe mosaic virus; Barley yellow dwarf virus; Barley yellow mosaic virus; Bean common mosaic virus; Bean golden mosaic virus; Bean leaf roll virus; Bean pod mottle; Bean yellow mosaic virus; Bearded iris mosaic virus; Beet curly top virus; Beet leaf curl virus; Beet mosaic virus; Beet necrotic yellow vein virus; Beet pseudo yellows virus; Beet western yellows virus; Beet yellow stunt virus; Belladona mottle virus; Black rasberry latent virus; Blight (et analogues/en analoge); Blueberry leaf mottle virus; Broad bean wilt virus; Bromoviruses; Cacao swollen shoot virus; Cacao yellow mosaic virus; Cactus virus X; Cadan-cadang viroid; Camation cryptic virus; Camation etched ring virus; Camation latent virus; Camation mottle virus; Camation necrotic fleck virus; Camation ringspot virus; Camation vein mottle virus; Cassava common mosaic virus; Cauliflower mosaic virus; Chemy leafroll virus; Chemy rasp leaf virus; Chemy rasp leaf virus (American); Chemy rugose virus; Chrysanthemum B virus; Chrysanthenum stunt viroid; Citrus exocortis viroid; Citrus leaf rugose virus; Citrus mosoie virus; Citrus tristeza virus (European isolates); Citrus tristeza virus (non-European isolates); Citrus variegation virus; Citrus veinenation woody gall; Citrus viroids; Clover Yellow vein virus; Cocksfoot mild mosaic virus group; Cocksfoot streak virus; Cowpea mild mottle virus; Cucumber mosaic virus; Cucumber yellows virus; Cucumovirus satellites; Cymbidium mosaic virus; Dahlia mosaic virus; Dasheen mosaic virus; Dianthoviruses; Echtes Ackerbohnenmosaic virus; Elderberry carlavirus; Euphorbia mosaic virus; Florida tomato virus; Grapevine algerian latent virus; Grapevine bulgarian latent virus; Grapevine fanleaf virus; Grapevine flavescence dorée mycoplasm; Grapevine leafroll associated virus (I to V); Grapevine tunusian ringspot virus; Grapevine virus A; Grapevine yellow speckle viroids (I & II); Grapewine chrome mosaic virus; Heracleum latent virus; Hippeastrum mosaic virus; Honeysuckle latent virus; Hop (American) latent virus; Hop latent virus; Hop mosaic virus; Hop stunt viroids; Hop virus A; Hop virus C; Hydrangea ringspot virus; Iliaviruses; Iris mild mosaic virus; Leek yellow stripe virus; Leprosis; Lettuce infectious yellows virus; Lettuce mosaic virus; Lilac chlorotic leafspot virus; Lilac ring mottle virus; Lilly symptomless virus; Luteovirus satellites; Maize dwarf mosaic virus; Maize streak virus; Marafiviruses; Melon necrotic spot virus; Myrobolan latent ringspot virus; Narcissus latent virus; Narcissus mosaic virus; Narcissus tip necrosis virus; Narcissus yellow stripe virus; Oat golden stripe virus; Oat mosaic virus; Odontoglossum ringspot virus; Olive latent ringspot virus; Onion yellow dwarf virus; Papaya mosaic virus; Papaya ringspot virus; Parsnip yellow fleck virus; Pea early browning virus; Pea enation mosaic virus; Pea seed borne mosaic virus; Peach mosaic virus (American); Pear decline mycoplasm; Pelargonium leaf curl virus; Pepper mild tigré virus; Plant reoviruses; Plum line pattern virus (American); Plum pox virus; Poinsettia mosaic virus; Poplar mosaic virus; Potato aucuba mosaic virus; Potato black ringspot virus; Potato leafroll virus; Potato leafroll virus (non European isolates); Potato mop-top virus; Potato spindle tuber viroid; Potato virus A; Potato virus A (non European isolates); Potato virus M; Potato virus M (non european isolates); Potato virus S; Potato virus S (non European isolates); Potato virus T; Potato virus X; Potato virus X (non European isolates); Potato virus Y; Potato virus Y (non European isolates); Potato yellow dwarf virus; Potato yellow mosaic virus; Prune dwarf virus; Prunus necrotic ringspot virus; Raspberry bushy dwarf virus; Raspberry leaf curl virus (American); Raspberry ringspot virus; Raspberry vein chlorosis virus; Red clover mottle virus; Red clover vein mosaic virus; Ribgrass mosaic virus; Rice stripe virus group; Rubus yellow net virus; Saguro cacao virus; Satellites (andere dan geciteerde); Satsuma dwarf virus; Shallot latent virus; Sharka virus; Sobemoviruses; Sowbane mosaic virus; Sowthistle yellow vein virus; Spinach latent virus; Squash leaf curl virus; Stolbur mycoplasm; Strawberry crinkle virus; Strawberry latent C virus; Strawberry latent ringspot virus; Strawberry mild yellow edge virus; Strawberry vein banding virus; Sugar beet yellows virus; Tater leaf virus; Tobacco etch virus; Tobacco mosaic virus; Tobacco necrosis virus; Tobacco rattle virus; Tobacco ringspot virus; Tobacco streak virus; Tobacco stunt virus; Tomato apical stunt viroid; Tomato aspermy virus; Tomato black ring virus; Tomato bunchy top viroid; Tomato bushy stunt virus; Tomato mosaic virus; Tomato planta macho viroid; Tomato ringspot virus; Tomato spotted wilt virus; Tomato yellow leaf curt virus; Tulare apple mosaic virus; Tulip breaking virus; Turnip crinkle virus satellites; Turnip crinkle virus; Turnip mosaic virus; Turnip yellow mosaic virus; Tymoviruses; Velvet tobacco mottle virus; other Viroids; Watermelon mosaic virus 2; Wheat dwarf virus; Wheat soil-bome mosaic virus; Wheat spindle steak mosaic virus; Wheat yellow mosaic virus; White clover mosaic virus; Yam mosaic virus; Zucchini yellow fleck virus; and Zucchini yellow mosaic virus.
The pest organism can be any species. Preferably, the pest organism is any insect or nematode of economic importance, such as, for example, organisms that cause disease, a household pest, or an agricultural pest, or that are associated with plants diseases, e.g. in corn, potatoes, soybeans, sugarbeets, turf, trees, orchards and vineyards, garden vegetables, etc.
The pest organism can be at any stage of development, however, it is preferred that when the organism is an insect, it is in a larval or adult developmental stage when the dsRNA is delivered.
In another embodiment, the invention relates to nucleic acids encoding the RNA delivery molecule and encoding the chimeric RNAi molecules as described herein.
According to a further aspect of the present invention, there are provided expression constructs, also referred herein as recombinant DNA constructs, to facilitate introduction into a host cell and for instance a plant cell and/or facilitate expression and/or facilitate maintenance of the nucleotide sequence encoding the RNA delivery molecules and/or the chimeric RNAi molecules according to the invention. The expression constructs may be inserted into a plasmid or a vector, which may be commercially available.
According to an embodiment of the present invention, the expression construct is an expression vector, suitable for transformation into host organisms such as yeast, bacteria, fungi or plants or plant cells and suitable for maintenance and expression of an RNA delivery molecule or a chimeric RNAi molecule according to the present invention in a transformed host cell. An “expression vector” is a construct that can be used to transform a selected host cell and provides for expression of a coding sequence in the selected host. Expression vectors can for instance be cloning vectors, binary vectors or integrating vectors. The invention thus also relate to a vector comprising any of the nucleic acids described above. Said vector may further comprise regulatory sequences for controlling expression of the nucleic acid in said host cell.
According to one embodiment of the present invention, the expression construct is a plant expression vector, suitable for transformation into plants and suitable for maintenance and expression of an RNA delivery molecule or a chimeric RNAi molecule according to the present invention in a transformed plant cell. The invention thus also relates to a vector comprising any of the nucleic acids described above. Said vector may further comprise regulatory sequences for controlling expression of the nucleic acid in a plant cell.
The terms “regulatory sequences” and “control sequence” used herein are to be taken in a broad context and refer to regulatory nucleic acid sequences capable of driving and/or regulating expression of the sequences to which they are ligated and/or operably linked. The control sequences differ depending upon the intended host organism and upon the nature of the sequence to be expressed. For expression of a protein in prokaryotes, the control sequences generally include a promoter, a ribosomal binding site, and a terminator. In eukaryotes, control sequences generally include promoters, terminators and, in some instances, enhancers, and/or 5′ and 3′ untranslated sequences. The term ‘control sequence’ is intended to include, at a minimum, all components necessary for expression, and may also include additional advantageous components. According to one embodiment of the present invention, the control sequence is operable in a plant; preferably the control sequence is a sequence derived from a plant sequence. The term “control sequence” encompasses a promoter or a sequence capable of activating or enhancing expression of a nucleic acid molecule in a cell, tissue or organ.
Promoters useful for the expression of dsRNA are a promoter from an RNA Poll, an RNA PollI, an RNA PollII, T7 RNA polymerase or SP6 RNA polymerase. These promoters are typically used for in vitro-production of dsRNA, which dsRNA is then included in an antipesticidal agent, for example in an anti-pesticidal liquid, spray or powder.
Examples of promoters suitable for the constructs and methods according to the present invention are constitutive plant promoters, such as the CaMV35S promoter, doubled CaMV35S promoter, GOS2 promoter, Figwort mosaic viruse (FMV) 34S promoter, rubisco promoter, actin promoter or ubiquitin promoter.
In order to improve the transfer of the dsRNA from the plant cell to the plant pest, the plants preferably express the dsRNA in plant parts easily accessible to the plant pest. Preferred tissues to express the dsRNA in are the roots, leafs, stems, rhizomes, shoots, tubers, anthers, petioles, seeds, flowers, fruits. Therefore, tissue-preferred promoters may be used, such as a root specific promoter or a leaf specific promoter. Suitable examples of a root preferred promoter are PsMTA (Fordam-Skelton, A. P., et al., 1997 Plant Molecular Biology 34: 659-668), Class III Chitinase promoter, etc. . . . Examples of leaf- and stem-specific or photosynthetic tissue-specific promoters that are also photoactivated are promoters of two chlorophyll binding proteins (cab1 and cab2) from sugar beet (Stahl D. J., et al., 2004 BMC Biotechnology 2004 4:31), ribulose-bisphosphate carboxylase (Rubisco), encoded by rbcS (Nomura M. et al., 2000 Plant Mol. Biol. 44: 99-106), A (gapA) and B (gapB) subunits of chloroplast glyceraldehyde-3-phosphate dehydrogenase (Conley T. R. et al. 1994 Mol. Cell. Biol. 19: 2525-33; Kwon H. B. et al. 1994 Plant Physiol. 105: 357-67), promoter of the Solanum tuberosum gene encoding the leaf and stem specific (ST-LS1) protein (Zaidi M. A. et al., 2005 Transgenic Res. 14:289-98), stem-regulated, defense-inducible genes, such as JAS promoters (patent publication no. 20050034192/US-A1), flower-specific promoters such as chalcone synthase promoter (Faktor O. et al. 1996 Plant Mol. Biol. 32: 849) and fruit-specific promoters such as that of RJ39 from strawberry (WO 98 31812). Other suitable promoters are pathogen-induced promoters, such as nematode induced plant promoters, or feeding-site specific promoters, examples of which are Wun-1 (Hansen et al. 1996. Physiol. Mol. Plant. Pathol. 48: 161-170); Lea-14, Lemmi 9 (Van der Eycken W et al. Plant J. 1996 9(1): 45-54; Escobar C et al. Mol Plant Microbe Interact. 1999, 12(5):440-9), pin-2 (Keil et al. 1989. EMBO J. 8:1323-1330) and TobRB7 (Opperman et al. 1994. Science, 263: 221-223). According to one embodiment of the invention, the vectors comprise a constitutive promoter. According to another embodiment of the invention, the vectors comprise an inducible promoter. According to another embodiment of the invention, the vectors comprise a tissue-specific promoter, for instance a root-specific promoter in case of alleviating pest infestations where the pest predominantly feeds on the roots of the plant, or for instance a leaf-specific promoter in case of alleviating pest infestations where the pest predominantly feeds on the leafs of the plant. Promoters which initiate transcription only in certain tissues or cells are herein referred to ‘tissue-specific or “cell-specific” promoters, respectively. In addition, the present invention relates to a vector according to the invention wherein the promoter is selected from the group comprising tissue specific promoters such as any selected from the group comprising root specific promoters of genes encoding PsMTA Class III Chitinase, photosynthetic tissue-specific promoters such as promoters of cab1 and cab2, rbcS, gapA, gapB and ST-LS1 proteins, JAS promoters, chalcone synthase promoter and the promoter of RJ39 from strawberry.
Optionally, one or more transcription termination sequences may also be incorporated in the expression construct. The term “transcription termination sequence” encompasses a control sequence at the end of a transcriptional unit, which signals 3′ processing and poly-adenylation of a primary transcript and termination of transcription. Additional regulatory elements, such as transcriptional or translational enhancers, may be incorporated in the expression construct.
The expression constructs of the invention may further include an origin of replication which is required for maintenance and/or replication in a specific cell type. One example is when an expression construct is required to be maintained in a bacterial cell as an episomal genetic element (e.g. plasmid or cosmid molecule). Preferred origins of replication include, but are not limited to the f1-ori and colE1 oh.
The expression construct may optionally comprise a selectable marker gene. As used herein, the term “selectable marker gene” includes any gene, which confers a phenotype on a cell in which it is expressed to facilitate the identification and/or selection of cells which are transfected or transformed with an expression construct of the invention.
Suitable markers may be selected from markers that confer antibiotic or herbicide resistance or visual markers. Examples of selectable marker genes include genes encoding neomycin phosphotransferase (nptII), hygromycin phosphotransferase (hpt) or Basta. Further examples of suitable selectable marker genes include resistance genes against ampicillin (Ampr), tetracydine (Tcr), kanamycin (Kanr), phosphinothricin, and chloramphenicol (CAT). Other suitable marker genes provide a metabolic trait, for example manA. Visual marker genes may also be used and include for example beta-glucuronidase (GUS), luciferase and Green Fluorescent Protein (GFP).
According to a preferred embodiment of the invention, the RNA delivery molecule and/or the chimeric RNAi molecules are expressed in plant cell organelles to protect dsRNA from processing.
According to a further embodiment, the nucleic acids encoding the RNA delivery molecule and/or the chimeric RNAi molecules may further comprise an in frame signal sequence for directing the encoded polypeptide to a plant organel, such as a chloroplast, a plastide, or a mitochondrion, for instance signaling the chimeric RNAi molecule towards an intracellular compartment of the host cell in another mechanism to protect dsRNA from processing
For example, the RNA delivery molecule, and/or the chimeric RNAi molecule, and/or the complex between the RNA delivery molecule and the chimeric RNAi molecule can be compartmentalized in an intermediate host cell or organism before it is transferred to the target host cell, e.g. a pest cell. It shall be understood that the RNA delivery molecule and the chimeric RNAi molecule may be directed to the same or to different organelles of an intermediate host cell.
In particular, the RNA delivery molecule, and/or the chimeric RNAi molecule, and/or the complex between the RNA delivery molecule may be compartmentalized in a plant cell, for instance it may be located in the chloroplast, mitochondrion or plastid, before it is transferred to the plant pest species, for example a plant pest nematode or insect. Compartmentalization may occur in a variety of ways, such as for example via the use of viroid structures, or via the use of signal sequences as described above, for example chloroplast, mitochondrial or plastid signal sequences. These organelles are form prokaryotic origin and may offer a protective environment away from the plant RNA processing machinery.
A major advantage of compartmentalization of the RNA delivery molecule, and/or the chimeric RNAi molecule, and/or the complex between the RNA delivery molecule thus include that the molecules of the complex are protected from nuclear/cytoplasmic processing (dicing) of dsRNA. In addition, compartmentalization provides for an accumulation of dsRNA sequences.
In yet another mechanism to protect the dsRNA contained within the chimeric RNAi molecule from RNA processing is to express sense and antisense separately and to target them to different locations within the host cell or organism that expresses the sense and the antisense strands. In the context of the present invention, the sense or the antisense strand is part of the chimeric RNAi molecule. In this embodiment, sense and antisense RNA fragments corresponding to a selected gene of a particular pest species are cloned behind different promoters driving expression (i) separate plant tissues or (ii) within the same cell but in separate cellular compartments. These promoters are tissue or organel specific and allow strong simultaneous expression in different cellular compartments or in adjacent tissues.
For example, the sense and antisense strands may be targeted to different plant tissue or cell types. For example, in a leaf the sense strand may be expressed in the nerve cells while the antisense is expressed in the palisade tissue. This may be achieved by using different promoters to drive the expression of the sense and the antisense strands. The advantage of this technique is that the sense and antisense strands never come together in the plant cell, and therefore no degradation or auto-silencing or RNA interference can occur within the plant by Dicer. When the pest organism feeds on the plant, the strands are set free and mixed, allowing the annealing of the dsRNA in the gut lumen and then base pairing between the sense and antisense strands may occur to form long dsRNA. Subsequently, this dsRNA may be taken up efficiently and leads to the desired RNAi response, leading to degradation of the target mRNA in the pest and death of the pest. This approach can be accomplished by feeding the pest with two bacterial strains for instance provided in a composition, one strain producing the sense, the other producing the antisense strand.
In another embodiment, the present invention relates to a host cell or organism comprising a nucleic acid or a vector as defined herein. Examples of host cells which may be used in accordance with the present invention include a bacterial, yeast, fungal, or plant cell. Host cells may be prokaryotic cells such as E. coli and A. tumefaciens, or may be eukaryotic cells such as yeast, or plant cells. It is preferred that host cells are monocotyledonous or dicotyledonous plant cells.
Accordingly, the present invention also encompasses a cell, e.g. a host cell, comprising any of the chimeric RNAi molecules, RNA delivery molecule, dsRNA, nucleic acid or a vector as defined herein. The invention further encompasses prokaryotic cells (such as, but not limited to, gram-positive and gram-negative bacterial cells) and eukaryotic cells (such as, but not limited to, yeast cells or plant cells). Preferably, said cell is a bacterial cell or a plant cell. The present invention also encompasses a transgenic plant, reproductive or propagation material for a transgenic plant comprising such a plant cell.
The vector or nucleic acid molecule according to the invention may either be integrated into the genome of the host cell or it may be maintained in some form extrachromosomally.
In another aspect, the present invention relates to a complex comprising:
In another embodiment, the present invention relates to a complex comprising:
It is to be understood that said complex is provided in such a condition that binding may occur between said RNA delivery molecule and said chimeric RNAi molecule. This complex is also referred to in the present invention as the “protein-RNA complex” or the “complex between the RNA delivery molecule and the chimeric RNAi”, or the “RNA vehicle complex (RVC)”.
It should be understood that in the above-described complexes of the invention comprising both an RNA delivery molecule and a chimeric RNAi molecule, the sequences of the molecules should be such that the RNA binding protein or RNA binding domain in the RNA delivery molecule recognizes and is able to bind to the RNA recognition site, specific for the RNA binding protein or RNA binding domain, in the chimeric RNAi molecule.
In one specific embodiment, the invention relates to a complex between an RNA delivery molecule and a chimeric RNAi molecule, wherein the RNA-binding domain of the RNA delivery molecule comprises the coliphage HK022 Nun protein or a fragment thereof, said fragment comprising the RNA-binding domain of the HK022 Nun protein, and wherein the chimeric RNAi molecule comprising the double stranded RNA molecule further comprises a nucleotide sequence corresponding to the binding motif for binding to the coliphage HK022 Nun protein or the fragment thereof. In a preferred embodiment, the RNA-binding domain is a polypeptide comprising the sequence represented in any of SEQ ID NOs 2, 4, 6, 8 or 87, most preferably comprising the sequence represented in SEQ ID NO 8, and the chimeric RNAi molecule comprising the double stranded RNA further comprises the binding motif represented in SEQ ID NO 15 or 16. In another preferred embodiment, the RNA-binding domain is a polypeptide comprising the sequence represented in any of SEQ ID NOs 2, 4, 6, 8 or 87, most preferably comprising the sequence represented in SEQ ID NO 8, and the chimeric RNAi molecule is any of the chimeric RNAi molecules as represented by any of SEQ ID NOs 45 to 48, 55, 61 to 64, 70, 76 to 79, and 85.
In another preferred embodiment, the invention relates to a complex between an RNA delivery molecule and a chimeric RNAi molecule wherein the RNA-binding domain of the RNA delivery molecule is the Bacillus subtilis LicT protein or a fragment thereof, said fragment comprising the RNA binding domain and wherein the chimeric RNAi molecule comprising the double stranded RNA molecule comprises a nucleotide sequence corresponding to the binding motif for binding to the Bacillus subtilis LicT protein or the fragment thereof. In a preferred embodiment the RNA binding domain is a polypeptide comprising the sequence represented in SEQ ID NO 10 or 12, preferably a polypeptide comprising the sequence represented in SEQ ID NO 12, and the chimeric RNAi molecule comprising the double stranded RNA molecule comprises the binding motif represented in
In yet another preferred embodiment, the invention relates to a complex between an RNA delivery molecule and a chimeric RNAi molecule wherein the RNA-binding domain of the RNA delivery molecule is MS2 or a fragment thereof, said fragment comprising the RNA binding domain and wherein the chimeric RNAi molecule comprising the double stranded RNA molecule comprises a nucleotide sequence corresponding to the binding motif for binding to MS2 or the fragment thereof. In a preferred embodiment, the RNA binding domain is a polypeptide comprising the sequence represented in SEQ ID NO 14 and the chimeric RNAi molecule comprising the double stranded RNA molecule comprises the binding motif represented in
Table 5 provides an overview of specific embodiments of complexes according to the invention comprising an RNA delivery molecule showing a specific RNA binding domain, combined with a chimeric RNAi molecule comprising RNA sequences that are recognized by said specific RNA binding domain of the RNA delivery molecule as indicated in Table 5.
Table 6 provides an overview of other specific embodiments of complexes according to the invention comprising an RNA delivery molecule containing an RNA binding domain, combined with a specific chimeric RNAi molecule as indicated in Table 6.
It shall be understood from the present description that the present RNA delivery molecules are particularly suitable for improving the delivery of dsRNA to pest organisms which are feeding on a plant expressing dsRNA for the purpose of eliciting RNA interference in the pest organism.
In one embodiment the present invention relates to an RNA delivery molecule comprising a fusion protein which consists of an RNA binding domain fused, preferably by means of a linker polypeptide, to a targeting module. Preferably said targeting module comprises a domain that is endocytosed in the gut of a target organism. The present RNA delivery molecule is capable of forming a complex with the chimeric RNAi molecule comprising dsRNA for the purpose of interference.
In another embodiment the present invention relates to an RNA delivery molecule comprising a fusion protein which consists of an RNA binding domain fused preferably by means of a linker polypeptide, to a domain that is transcytosed from the gut to the haemolymph or coelumic fluid of a target organism. The present RNA delivery molecule is capable of forming a complex with the chimeric RNAi molecule comprising dsRNA for the purpose of interference.
The present invention relates to methods for delivering dsRNA to a pest species, to methods for down-regulating the expression of a target gene in a pest species and to methods for producing transgenic plants resistant to pest species.
Methods according to the present invention include feeding the RNA delivery molecules to the organism to deliver the dsRNA to the organism tissues. It is envisaged that the methods of the invention will have use in controlling plant diseases caused by feeding organisms. Methods of pest control of organisms, and of protecting plants against organisms are provided.
The RNA delivery molecule and the dsRNA for purposes of RNA interference may be taken up by the pest organism in several ways.
The invention relates to methods for delivering one or more double-stranded RNA molecules to a pest species, comprising:
In another embodiment, a method is provided for delivering double-stranded RNA to a pest species, comprising feeding the pest species with a mixture of an RNA molecule and an RNA delivery molecule according to the present invention,
In one embodiment the invention also relates to a method for down-regulating expression of a target gene in a pest species, comprising feeding the pest species with a mixture of an RNA molecule and an RNA delivery molecule according to the present invention,
In yet another embodiment, a method is provided for delivering double-stranded RNA to a pest species, comprising feeding the pest species with a complex comprising an RNA delivery molecule as defined herein, and at least one chimeric RNAi molecule consisting of an RNA molecule wherein the RNA molecule comprises double-stranded RNA comprising annealed complementary strands, one of which has a nucleotide sequence which is complementary to at least part of a target nucleotide sequence of the target gene to be down-regulated, and further comprises a sequence which binds to the RNA-binding domain of the RNA delivery molecule,
The term “feeding” according to the present invention may refer to feeding of the pest species with a host cell or organism, e.g. plant cell, bacteria, fungi, yeast, etc., or a mixture thereof comprising or expressing, sprayed with or coated with at least one RNA delivery molecule and/or chimeric RNAi molecule of the invention. In one embodiment, a mixture of bacteria or plant(s) cell(s) may be fed to a pest species, whereby the mixture comprises at least one bacterium or plant (cell) that comprises or expresses an RNA delivery molecule and at least another bacterium or plant (cell) that comprises or expresses a chimeric RNAi molecule.
In yet another embodiment, the invention relates to a method for down-regulating expression of a target gene in a pest species, comprising:
In more specific embodiments, the invention relates to any of the methods described above wherein the RNA-binding domain of an RNA delivery molecule (a) comprises the coliphage HK022 Nun protein or a fragment thereof, said fragment comprising the RNA-binding domain of the HK022 Nun protein, and wherein the double stranded RNA molecule (b) comprises a nucleotide sequence corresponding to the binding motif for binding to the coliphage HK022 Nun protein or the fragment thereof. Even more specific, the invention relates to such a method wherein the RNA-binding domain is a polypeptide comprising the sequence represented in any of SEQ ID NOs 2, 4, 6, 8 or 87, preferably comprising the sequence represented in SEQ ID NO 8, and wherein the double stranded RNA molecule (b) comprises the binding motif represented in SEQ ID NO 15 or 16.
In other specific embodiments, the invention relates to any of the methods described above wherein in (a) the RNA binding domain is the Bacillus subtilis LicT protein or a fragment thereof, said fragment comprising the RNA binding domain and wherein the double stranded RNA molecule (b) comprises a nucleotide sequence corresponding to the binding motif for binding to the Bacillus subtilis LicT protein or the fragment thereof. Even more specific, the invention relates to such a method wherein the RNA binding domain is a polypeptide comprising the sequence represented in SEQ ID NO 10 or 12, preferably a polypeptide comprising the sequence represented in SEQ ID NO 12, and wherein the double stranded RNA molecule (b) comprises the binding motif represented in
In other specific embodiments, the invention relates to any of the methods described above wherein in (a) the RNA binding polypeptide is MS2 or a fragment thereof said fragment comprising the RNA binding domain and double stranded RNA molecule (b) comprises a nucleotide sequence corresponding with the binding motif for binding to MS2 or the fragment thereof. Even more specific, the invention relates to such a method wherein in (a) the RNA binding domain is a polypeptide comprising the sequence represented in SEQ ID NO 14, and wherein (b) comprises the binding motif represented in
A method for producing a transgenic plant that is resistant to a pest species, comprising:
In more specific embodiments, the invention relates to any of the methods described above for producing a transgenic plant that is resistant to a pest species, wherein the RNA-binding domain of an RNA delivery molecule (a) comprises the coliphage HK022 Nun protein or a fragment thereof, said fragment comprising the RNA-binding domain of the HK022 Nun protein, and wherein the double stranded RNA molecule (b) comprises a nucleotide sequence corresponding to the binding motif for binding to the coliphage HK022 Nun protein or the fragment thereof. Even more specific, the invention relates to such a method wherein the RNA-binding domain is a polypeptide comprising the sequence represented in any of SEQ ID NOs 2, 4, 6, 8 or 87, preferably comprising the sequence represented in SEQ ID NO 8, and wherein the double stranded RNA molecule (b) comprises the binding motif represented in SEQ ID NO 15 or 16.
In other specific embodiments, the invention relates to any of the methods described above for producing a transgenic plant that is resistant to a pest species wherein in (a) the RNA binding domain is the Bacillus subtilis LicT protein or a fragment thereof, said fragment comprising the RNA binding domain and wherein the double stranded RNA molecule (b) comprises a nucleotide sequence corresponding to the binding motif for binding to the Bacillus subtilis LicT protein or the fragment thereof. Even more specific, the invention relates to such a method wherein the RNA binding domain is a polypeptide comprising the sequence represented in SEQ ID NO 10 or 12, preferably a polypeptide comprising the sequence represented in SEQ ID NO 12, and wherein the double stranded RNA molecule (b) comprises the binding motif represented in
In other specific embodiments, the invention relates to any of the methods described above for producing a transgenic plant that is resistant to a pest species wherein in (a) the RNA binding polypeptide is MS2 or a fragment thereof said fragment comprising the RNA binding domain and double stranded RNA molecule (b) comprises a nucleotide sequence corresponding with the binding motif for binding to MS2 or the fragment thereof. Even more specific, the invention relates to such a method wherein in (a) the RNA binding domain is a polypeptide comprising the sequence represented in SEQ ID NO 14, and wherein (b) comprises the binding motif represented in
In yet another embodiment, the method for producing a transgenic plant that is resistant to a pest species, comprises:
Even more specific, the invention relates to such a method for producing a transgenic plant that is resistant to a pest species wherein said chimeric RNAi molecule is a molecule as described in Example 2. According to further specific embodiments, the invention relates to such a method for producing a transgenic plant that is resistant to a pest species wherein said chimeric RNAi molecule has a sequence as represented any of
Thus, the present invention provides for methods for the production of transgenic plants, plant cells or plant tissues comprising the introduction of a nucleic acid or vector according to the invention into the genome of said plant, plant cell or plant tissue.
The present invention also relates to a transgenic plant resistant to a pest species, an essential derived variety thereof, plant part, plant cell or protoplast thereof obtainable by any of the methods as described herein.
In another embodiment, the invention relates to a transgenic plant, essentially derived variety thereof, plant part, plant cell or protoplast thereof which comprises a nucleic acid encoding an RNA delivery molecule as defined herein, wherein said nucleic acid is heterologous to the genome of said transgenic plant, or an essentially derived variety thereof, plant part, plant cell or plant protoplast thereof.
The invention also relates to a transgenic plant, essentially derived variety thereof, plant part, plant cell or protoplast thereof which comprises a nucleic acid encoding an RNA delivery molecule as defined herein, and which comprises a nucleic acid encoding a chimeric RNAi molecule as defined herein, wherein said nucleic acids are heterologous to the genome of said transgenic plant, or an essentially derived variety thereof, plant part, plant cell or plant protoplast thereof.
In yet another embodiment, the invention provides a transgenic plant which comprises a vector as described herein.
As used herein, ‘transgenic plant’ includes reference to a plant, which comprises within its genome a heterologous polynucleotide. Generally, the heterologous polynucleotide is stably integrated within the genome such that the polynucleotide is passed on to successive generations. The heterologous polynucleotide may be integrated into the genome alone or as part of a vector. ‘Transgenic’ is used herein to include any cell, cell line, callus, tissue, plant part or plant, the genotype of which has been altered by the presence of the heterologous nucleic acid including those transgenics initially so altered as well as those created by sexual crosses or asexual propagation from the initial transgenic.
In another embodiment of the invention, there is provided a plant, essentially derived variety thereof, plant part, plant cell or protoplast thereof wherein the plant, essentially derived variety thereof, plant part, plant cell, or protoplast thereof has been transformed with a nucleic acid encoding an RNA delivery molecule as defined herein, and optionally also with a nucleic acid encoding a corresponding chimeric RNAi molecule as described herein.
The present invention also provides a plant, essentially derived variety thereof, plant part, plant cell, or protoplast thereof which co-expresses:
In another embodiment of the invention also provides a plant, essentially derived variety thereof, plant part, plant cell, or protoplast thereof which co-expresses:
Even more specific, the invention relates to a plant, essentially derived variety thereof, plant part, plant cell, or protoplast thereof which co-expresses an RNA delivery molecule as defined herein, and a chimeric RNAi molecule according to the present invention, wherein said chimeric RNAi molecule has a sequence as represented any of
In one specific embodiment, the invention relates to a plant, essentially derived variety thereof, plant part, plant cell, or protoplast thereof which co-expresses an RNA delivery molecule as defined herein, and a chimeric RNAi molecule according to the present invention, wherein the RNA-binding domain of the RNA delivery molecule comprises the coliphage HK022 Nun protein or a fragment thereof, said fragment comprising the RNA-binding domain of the HK022 Nun protein, and wherein the chimeric RNAi molecule comprises a nucleotide sequence corresponding to the binding motif for binding to the coliphage HK022 Nun protein or the fragment thereof. In a preferred embodiment, the RNA-binding domain is a polypeptide comprising the sequence represented in any of SEQ ID NOs 2, 4, 6, 8 or 87, most preferably comprising the sequence represented in SEQ ID NO 8, and the chimeric RNAi molecule comprises the binding motif represented in SEQ ID NO 15 or 16. In another preferred embodiment, the RNA-binding domain is a polypeptide comprising the sequence represented in any of SEQ ID NOs 2, 4, 6, 8 or 87 most preferably comprising the sequence represented in SEQ ID NO 8, and the chimeric RNAi molecule is any of the chimeric RNAi molecules as represented by any of SEQ ID NOs 45 to 48, 55, 61 to 64, 70, 76 to 79, and 85.
In another specific embodiment, the invention relates to a plant, essentially derived variety thereof, plant part, plant cell, or protoplast thereof which co-expresses an RNA delivery molecule as defined herein, and a chimeric RNAi molecule according to the present invention, wherein the RNA-binding domain of the RNA delivery molecule is the Bacillus subtilis LicT protein or a fragment thereof, said fragment comprising the RNA binding domain and wherein the chimeric RNAi molecule le comprises a nucleotide sequence corresponding to the binding motif for binding to the Bacillus subtilis LicT protein or the fragment thereof. In a preferred embodiment the RNA binding domain is a polypeptide comprising the sequence represented in SEQ ID NO 10 or 12, preferably a polypeptide comprising the sequence represented in SEQ ID NO 12, and the chimeric RNAi molecule comprises the binding motif represented in
In yet another specific embodiment, the invention relates to a plant, essentially derived variety thereof, plant part, plant cell, or protoplast thereof which co-expresses an RNA delivery molecule as defined herein, and a chimeric RNAi molecule according to the present invention, wherein the RNA-binding domain of the RNA delivery molecule is MS2 or a fragment thereof, said fragment comprising the RNA binding domain and wherein the chimeric RNAi molecule comprises a nucleotide sequence corresponding to the binding motif for binding to MS2 or the fragment thereof. In a preferred embodiment, the RNA binding domain is a polypeptide comprising the sequence represented in SEQ ID NO 14 and the chimeric RNAi molecule comprises the binding motif represented in
The term “transformation” as used herein, refers to the transfer of an exogenous polynucleotide into a host cell, irrespective of the method used for the transfer. The polynucleotide may be transiently or stably introduced into the host cell or organism and may be maintained non-integrated, for example, as a plasmid, or alternatively, may be integrated into the host genome. Transformation may be transient or stable. The invention thus also relates to such a stably or transiently transformed transgenic plant, plant cell or plant tissue. The invention further relates to any plant which comprises any of the subject vectors in accordance with the invention.
According to a further embodiment, the invention also relates to any of the transgenic plants described herein comprising a nucleic acid encoding an RNA delivery molecule as defined herein characterized in that said plant has increased resistance to a pest organism, for instance increased resistance of between 30% to 80% compared to control plants.
In other embodiments, the invention also relates to the progeny of a plant or essentially derived variety thereof obtainable by a method of the present invention or as described herein which has been obtained in a generative or vegetative manner.
The present invention also includes parts or derivatives of obtainable by a method of the present invention or as described herein, such as but not limited to leaves, stems, roots, shoots, cuttings or explants and the like, protoplasts, somatic embryos, anthers, petioles, cells in culture, seeds, flowers, fruits and tubers.
In another embodiment the invention relates to a method for controlling a pest species comprising feeding said pest species with a mixture of an RNA molecule and an RNA delivery molecule as defined herein,
In yet another embodiment the invention relates to a method for controlling a pest species comprising feeding the pest species with a complex comprising an RNA delivery molecule as defined herein, and at least one chimeric RNAi molecule consisting of an RNA molecule wherein the RNA molecule comprises double-stranded RNA comprising annealed complementary strands, one of which has a nucleotide sequence which is complementary to at least part of a target nucleotide sequence of the target gene to be down-regulated, and further comprises a sequence which binds to the RNA-binding domain of the RNA delivery molecule,
In yet another embodiment the invention also relates to a method for controlling a pest species comprising feeding the pest species with a transgenic plant or any progeny or part thereof as defined herein which is resistant to said pest species.
In yet another embodiment a method is provided for protecting a plant against a pest organism comprising co-expressing in said plant of:
In yet another embodiment a method is provided for protecting a plant against a pest organism comprising co-expressing in said plant:
Even more specific, said chimeric RNAi molecule has a sequence as represented in any of
The invention further relates to any of the methods described herein wherein the said pest species is any pest species described herein.
In a preferred embodiment the host organism is a plant and the pest species is a plant pathogenic pest.
The term “plant” as used herein encompasses any plant material such as inter alia a plant cell, plant tissue (including callus), plant part, whole plant, ancestors and progeny. A plant part may be any part or organ of the plant and include for example a seed, fruit, stem, leaf, shoot, flower, anther, root or tuber. The plant material should express, or have the capability to express, RNA delivery molecules, chimeric RNAi molecules, and dsRNA corresponding to one or more target genes of the pest species to be killed or paralyzed. The term “plant” also encompasses suspension cultures, embryos, meristematic regions, callus tissue, gametophytes, sporophytes, pollen, and microspores. The plant as used herein refers to all plants including algae, ferns and trees. In a preferred embodiment the plant belongs to the superfamily of Viridiplantae, further preferably is a monocot or a dicot. According to one embodiment of the present invention, the plant is susceptible to infestation by a plant pathogenic and/or parasitic nematode, by a fungus or an insect. Particular plants useful in the methods of the present invention are crop plants including for example monocots such as sugar cane and cereals (including wheat, oats, barley, sorghum, rye, millet, corn, rice) and dicots such as potato, tomato, vine, apple, pear, banana, sunflower, soybean, canola, alfalfa, rapeseed and cotton. Particular trees that can be used in the methods of the present invention are pine, eucalyptus and poplar.
“Administering” a DNA to a cell may be achieved by a variety of means, each well known by the person skilled in the art. Examples of useful techniques are shot-gun, ballistics, electroporation, transfection and transformation. For particular embodiments of the present invention where the cell is a plant cell, general techniques for expression of exogenous double-stranded RNA in plants for the purposes of RNAi are known in the art (Baulcombe D, 2004, Nature. 431(7006):356-63. RNA silencing in plants the contents of which are incorporated herein by reference). General techniques for expression of proteins in plants are known in the art (Fischer R et al. 1999, Biotechno. Appl. Biochem. (Pt2) 99-101 and 101-108; or Cunningham C. 1997 (Ed.). Recombinant Proteins from Plants, 308p). More particularly, methods for expression of double-stranded RNA in plants for the purposes of down-regulating gene expression in plant pests such as nematodes or insects are also known in the art. Similar methods can be applied in an analogous manner in order to express the RNA delivery molecule and/or the chimeric RNAi molecule in plants for the purposes of down-regulating expression of a target gene in a plant pest species. In order to achieve this effect it is necessary only for the plant to express (transcribe) the RNA delivery molecule and/or the chimeric RNAi molecule in a part of the plant which will come into direct contact with the pest species, such that the RNA delivery molecule and/or the chimeric RNAi molecule (or the complex) can be taken up by the pest species. Depending on the nature of the pest species and its relationship with the host plant, expression of the RNA delivery molecule and/or the chimeric RNAi molecule could occur within a cell or tissue of a plant within which the pest species is also present during its life cycle, or the RNA delivery molecule and/or the chimeric RNAi molecule may be secreted into a space between cells, such as the apoplast, that is occupied by the pest species during its life cycle. Furthermore, the RNA delivery molecule and/or the chimeric RNAi molecule may be located in the plant cell, for example in the cytosol, or in the plant cell organelles such as chloroplast, mitochondrion, vacuole or endoplasmatic reticulum.
Alternatively, the RNA delivery molecule and/or the chimeric RNAi molecule may be secreted by the plant cell and by the plant to the exterior of the plant. As such, the RNA delivery molecule and/or the chimeric RNAi molecule may form a protective layer on the surface of the plant.
The present invention thus relates to a method for the production of a transgenic cell or organism, comprising the step of administering a molecule, nucleic acid or a vector as described herein to said cell or organism. Preferably, said cell is a plant cell or said organism is a plant. The invention further relates to any transgenic cell or transgenic organism obtainable by the above described method, preferably said transgenic cell or organism is plant cell or plant organism.
The methods of the present invention for the production of transgenic organism may further comprise the steps of cultivating the transgenic cell under conditions promoting growth and development. Where the transgenic organism is a plant, these methods may further comprise the steps of regenerating a plant from plant tissue, allowing growth to reach maturity and to reproduce. Alternatively, the transgenic plant tissue may take other forms or may form part of another plant, examples of which are chimera plants and grafts (for example a transformed rootstock grafted to an untransformed scion). Advantapes
Uses of the present RNA delivery molecule for delivering dsRNA from a plant to a feeding organism are numerous.
A first major advantage of the delivery system according to the present invention is that it permits to deliver dsRNA more efficiently intracellularly in target organisms. The present system enables the delivery and uptake of the chimeric RNAi molecules of the invention, comprising double stranded RNA for the purpose of RNA interference. The chimeric RNAi molecules may even comprise small RNA fragments, e.g. 21 mers, and efficiently deliver these to the gut cell of a target pest organism. Feeding a target organism dsRNA that has been bound to a delivery molecule according to the present invention and that is efficiently delivered results in an improved uptake of the dsRNA. As a result thereof, lower amounts of dsRNA need to be used in order to obtain a suitable effect in the target organism.
In the case that the RNA delivery molecule according to the present invention comprises a domain that binds a protein that is endocytosed in the gut of a target organism or that binds to an endocytosis receptor, the complex between the RNA delivery molecule and the chimeric RNAi molecule which is formed in the target organism or taken up by the target organism by feeding can enter the gut cells through endocytosis, e.g. by entering endocytic vesicles, and from there are capable of entering the cell cytoplasm. In the endosome the protein-RNA complex may be dissociated through proteolysis or pH-dependent dissociation. A fraction of the dsRNA will then enter the cell in a manner similar to the delivery mechanism for antisense RNAs, as is well known in the literature.
The gut of an insect is a hostile environment, having low or high pH values and RNases which degrade RNA. High pH such as found in lepidopteran guts degrades RNA chemically enhanced. Transcytosis of the RNA molecules to the haemolymph enables to quickly remove the dsRNA from an RNase rich and/or pH hostile environment. In the case that the RNA delivery molecule according to the present invention comprises a domain that binds a protein that is transcytosed through the gut of a target organism to the haemolymph or coelomic fluid, or that binds to a transcytosis receptor, the chimeric RNA molecules which are taken up by the target organism by feeding can enter the gut and pass through the gut to the haemolymph or coelomic fluid. Transcytosis of the chimeric RNAi molecules to the haemolymph or coelomic fluid allows to direct the dsRNA to a broad range of target tissues including muscles, CNS, and other.
In other cases, it may also be required to have a combination of endocytosis and transcytosis to have efficient and site-specific delivery of the dsRNA bound to the delivery molecule.
Another advantage of the present RNA delivery molecule is that when forming a complex with the dsRNA, it effectively protects the dsRNA molecules from degradation in the plant and in the gut of the target organism, which is a very hostile environment.
The present RNA delivery molecule may thus allow expression of long as well as short dsRNA fragments in plants, to be delivered by feeding to a target organism. Usually, long (of e.g. 80 bp or more) dsRNA fragments are expressed in a plant for delivery by feeding to a target organism. Expression of long dsRNA fragments involves several disadvantages. For instance, it makes it necessary to protect these long RNA fragments in the plant cytoplasm from Dicer activity in the endogenous plant. Dicing of longer RNA fragments may result in diced fragments that may create dominant negative effects in plants through tittering away RISC which is needed for normal plant growth and physiology, or which may down regulate plant genes or chromatic or even the transgenic dsRNA expressing gene. Smaller dsRNA molecules (even as short as 21 bp) may be effectively fed to target organisms and taken up in the gut enterocytes leading to target knockdown. As a consequence thereof, it may be not longer required to express long RNA fragments of 80 bp or longer in the plants and shorter—and thus more specific and selective—target fragments can be expressed in plants.
In addition, in the case long RNA fragments of 80 bp or longer are still to be expressed in the plants, using the present RNA delivery molecule which protect the RNA, may obviate the need of additionally protecting these fragments from dicing activity in the endogenous plant.
Another major advantage of the present delivery system is that the delivery molecule can be used for improving the delivery of chimeric RNAi molecules using a sequence or structure specific RNA binding protein. The present RNA delivery system can advantageously be used for binding different categories of RNA. In particular, the present system is capable of binding dsRNA generically, or dsRNA, ssRNA or RNA structures specifically, as long as they contain the recognition sequence or structure. In a preferred embodiment, the present RNA delivery system can be used to bind a chimeric RNAi consisting of a target specific region (target dsRNA) for the purpose of RNA interference, and an RNA sequence that specifically binds the RNA delivery molecule, and in particular the RNA binding domain thereof. Advantageously, in such case the dsRNA would not interact with plant Dicer. Use of a chimeric RNAi bound to the RNA delivery molecule of the present invention also allows the use of long RNA fragments in plants, which will not be processed to diced fragments that could induce negative side-effects in the plants as explained above. In addition, binding of a chimeric RNAi molecule to an RNA delivery molecule according to the present invention permits the transgenic dsRNA molecules to be accumulated in a selected compartment in the plant, and for instance in the nucleolus, nucleus, cytoplasm tRNA or ribosome, phloem, etc., which allows a more efficient protection, accumulation or delivery to a target organism.
In general, the present invention also relates to the use of RNA delivery molecules or complexes thereof with a chimeric RNAi molecule for various agronomic and research applications requiring the delivery of dsRNA into a target pest organism.
In an embodiment, the invention relates to the use of an RNA delivery molecule as described herein for delivering dsRNA to a pest species.
In another embodiment, the invention also relates to the use of an RNA delivery molecule in combination with a corresponding chimeric RNAi molecule as described herein for delivering dsRNA to a pest species.
It shall be understood from the present description that the present RNA delivery molecules are particularly suitable for improving the delivery of dsRNA to pest organisms which are feeding on a plant expressing dsRNA. Alternatively, it is apparent that the present RNA delivery molecules according to the present invention may also be very useful for improving the delivery of dsRNA to pest organisms by any other way, including but not limited to injection of dsRNA, soaking the organisms in dsRNA solution or by feeding the pest organisms Escherichia coli bacteria that simultaneously express sense and antisense RNAs and that can acquire dsRNA.
In yet another embodiment, the present invention relates to the use of RNA delivery molecules in combination with corresponding chimeric RNAi molecules for down-regulating the expression of target genes in pest species.
In another embodiment, the present complexes between RNA delivery molecules and corresponding chimeric RNAi molecules are also very useful for down-regulating the expression of target genes in pest species. The invention therefore also provides for the use of said complexes as described herein for down-regulating the expression of target genes in pest species.
In yet another embodiment, the invention relates to the use of an RNA delivery molecule as described herein for producing a transgenic plant.
In yet another embodiment, the present invention relates to the use of an RNA delivery molecule in combination with a chimeric RNAi molecule for producing transgenic plants resistant to pest organisms.
In another embodiment, the present complexes between an RNA delivery molecule and a corresponding chimeric RNAi molecule are also very useful for producing transgenic plants which are resistant to a pest species. The invention therefore also provides for the use of said complexes as described herein for producing transgenic plants resistant to pest organisms.
In more specific embodiments, the present invention relates to the use of a transgenic plant resistant to a pest organism as described herein for controlling pest population growth, and/or for reducing infestation by a pest species and/or for killing or paralyzing a pest organism, and/or for preventing or reducing the amount and the number of chemical (e.g. pesticide, fungicide, nematicide) applications, and/or for reducing the environmental impact of chemical applications pesticides and/or for reducing disease incidence in a crop and/or for improving crop yield.
In another embodiment the invention relates to the use of a plant, essentially derived variety thereof, plant part, plant cell or protoplast thereof that has been transformed with (i) a nucleic acid encoding an RNA delivery molecule and (ii) a nucleic acid encoding a corresponding chimeric RNAi molecule as herein described for improving resistance to a pest organism, and/or for controlling pest population growth, and/or for preventing or reducing infestation by a pest species and/or for killing or paralyzing a pest organism, and/or for reducing the amount and the number of chemical (e.g. pesticide, fungicide, nematicide) applications, and/or for reducing the environmental impact of chemical applications pesticides and/or for reducing disease incidence in a crop and/or for improving crop yield.
In yet another embodiment the invention relates to the use of a plant, essentially derived variety, plant part, plant cell or protoplast thereof which co-expresses:
In one specific embodiment, the invention relates to any of the uses as described above, wherein
In yet another specific embodiment, the invention relates to any of the uses as described above, wherein
In yet another embodiment, the invention relates to the use of progeny or parts or derivatives of plants obtainable from any plant or essentially derived variety thereof as described herein for improving resistance to pest organism, and/or for controlling pest population growth, and/or for preventing or reducing infestation by a pest species and/or for killing or paralyzing a pest organism, and/or for reducing the amount and the number of chemical (e.g. pesticide, fungicide, nematicide) applications, and/or for reducing the environmental impact of chemical applications pesticides and/or for reducing disease incidence in a crop and/or for improving crop yield.
In one other specific embodiment, the method of the invention may also be used as a tool for experimental research, particularly in the field of functional genomics. Targeted down-regulation of pest genes by RNAi can be used in in vitro or in vivo assays in order to study gene function. Assays based on targeted down-regulation of specific pest genes, leading to a measurable phenotype may also form the basis of compound screens for novel pesticides.
In a further aspect the invention relates to a composition for reducing pest population growth and/or for killing or paralyzing a pest organism and/or for improving plant resistance to pest organisms, for improving resistance to pest organism, and/or for controlling pest population growth, and/or for preventing or reducing infestation by a pest species and/or for killing or paralyzing a pest organism, for reducing disease incidence in a crop and/or for improving crop yield, said composition comprising at least one RNA delivery molecule as defined herein, and more preferably comprising at least one RNA delivery molecule and/or at least one chimeric RNAi molecule as herein described.
According to one embodiment, the invention relates to a composition comprising at least one RNA delivery molecule as defined herein, and more preferably comprising at least one RNA delivery molecule and/or at least one chimeric RNAi molecule as herein described and a physiological or agronomical acceptable carrier, excipient or diluent. The invention also encompasses the use of said composition as a pesticide for a plant or for propagation or reproductive material of a plant.
According to yet another embodiment, the invention relates to a composition comprising at least one RNA delivery molecule as defined herein, and more preferably comprising at least one RNA delivery molecule and/or at least one chimeric RNAi molecule as herein described, and a physiological or agronomical acceptable carrier, excipient or diluent.
The composition may contain further components which serve to stabilise the dsRNA and/or prevent degradation of the dsRNA during prolonged storage of the composition.
The composition may still further contain components which enhance or promote uptake of the RNA delivery molecule and/or the chimeric RNAi molecule by the pest organism. These may include, for example, chemical agents which generally promote the uptake of RNA into cells e.g. lipofectamin etc., and enzymes or chemical agents capable of digesting the fungal cell wall, e.g. a chitinase.
The composition may be in any suitable physical form for application to the pest, to substrates, to cells (e.g. plant cells), or to organism infected by or susceptible to infection by a pest species. In another embodiment, the invention provides a composition comprising:
The RNA molecule contained in said compositions may be (partially) self-complementary or comprise a sense and antisense strand forming a double stranded portion.
In another embodiment, the invention provides a composition comprising:
In yet another embodiment, the present invention relates to a composition comprising:
In one specific embodiment, the invention relates to a composition, ne specific embodiment, the invention relates to any of the uses as described above, wherein
HK022 Nun protein or a fragment thereof, said fragment comprising the RNA-binding domain of the HK022 Nun protein, preferably the RNA binding domain is a polypeptide comprising the sequence represented in any of SEQ ID NOs 2, 4, 6, 8 or 87, most preferably comprising the sequence represented in SEQ ID NO 8, and
In another specific embodiment, the invention relates to a composition, wherein
In yet another specific embodiment, the invention relates to a composition, wherein
In addition, the present invention also relates to methods for producing an RNA delivery molecule described herein comprising:
In a preferred embodiment the present invention relates to a method for producing an RNA delivery molecule, wherein the RNA binding domain of said delivery molecule comprises a polypeptide comprising the coliphage HK022 Nun protein (for instance as represented in SEQ ID NO 2), a homologue thereof, or a fragment thereof comprising the RNA-binding domain, said fragment preferably comprising amino acids 1 to 47 (SEQ ID NO 4) of the aminoterminal sequence, more preferably comprising amino acids 13 to 47 (SEQ ID NO 6) of the aminoterminal sequence, most preferably comprising amino acids 22 to 47 (SEQ ID NO 8) of the aminoterminal sequence of the HK022 Nun protein.
In another preferred embodiment the present invention relates to a method for producing an RNA delivery molecule, wherein the RNA binding domain of said delivery molecule comprises a polypeptide comprising the Bacillus subtilis LicT protein (for instance as represented in SEQ ID NO 10), a homologue thereof, or a fragment thereof comprising the RNA-binding domain, said fragment preferably comprising amino acids 1 to 56 (SEQ ID NO 12) of the aminoterminal sequence of the LicT protein.
In yet another preferred embodiment the present invention relates to a method for producing an RNA delivery molecule, wherein the RNA binding domain of said delivery molecule comprises a polypeptide comprising the bacteriophage MS2 coat protein (for instance as represented in SEQ ID NO 14), a homologue thereof, or a fragment thereof comprising the RNA-binding domain.
In addition, the present invention also relates to methods for producing a chimeric RNAi molecule described herein comprising:
isolating the chimeric RNAi molecule produced by the host cell.
In a preferred embodiment the present invention relates to a method for producing a chimeric RNAi molecule wherein the chimeric RNAi molecule comprises:
According to another preferred embodiment, the present invention relates to a method for producing a chimeric RNAi molecule wherein the chimeric RNAi molecule has a sequence as represented any of
In addition, the present invention also relates to methods for producing a complex comprising an RNA delivery molecule as defined herein, and at least one chimeric RNAi molecule as defined herein comprising:
In the context of preparing an RNA delivery molecule, a chimeric RNAi molecule or a complex comprising an RNA delivery molecule as defined herein, the term “host cell” may any prokaryotic or eukaryotic cell, such as a bacterial, insect, fungal, plant or animal cell. In more specific embodiment the invention relates to methods for producing specific complexes as represented in Table 3 or 4.
According to another embodiment, the present invention also relates to a kit comprising at least one RNA delivery molecule as described herein. According to yet another embodiment, the present invention also relates to a kit comprising at least one chimeric RNAi molecule as described herein. According to yet another embodiment, the present invention also relates to a kit comprising a nucleic acid encoding an RNA delivery molecule as described herein. The invention also relates to a kit comprising any vector described herein comprising a nucleic acid encoding any of the RNA delivery molecules and/or any of the corresponding RNAi molecule as described herein. It should be understood that these nucleic acid sequences according to the present invention may be comprised in one or in several separate vectors.
In another preferred embodiment, the invention relates to a kit comprising a composition or a complex as defined herein. Suitable combinations of specific RNA delivery molecule with chimeric RNAi molecule in such compositions or complexes are represented in Tables 5 and 6.
It is further contemplated that the “composition” of the invention may be supplied as a “kit-of-parts” comprising the RNA delivery molecule and the chimeric RNAi molecule in one or in separate containers, and a suitable diluent or carrier for the RNA in a further separate container. The invention also relates to the supply of the RNA delivery molecule and/or the chimeric RNAi molecule alone without any further components. In these embodiments the RNA delivery molecule and/or the chimeric RNAi molecule may be supplied in a concentrated form, such as a concentrated aqueous solution. It may even be supplied in frozen form or in freeze-dried or lyophilized form. The latter may be more stable for long term storage and may be de-frosted and/or reconstituted with a suitable diluent immediately prior to use.
The present invention further relates to the medical use of any of the delivery molecule, chimeric RNAi molecules, constructs, nucleotide sequences, recombinant DNA constructs or compositions thereof described herein.
In one specific embodiment, the composition is a pharmaceutical or veterinary composition for treating or preventing pest infections of humans or animals, respectively. Such compositions will comprise at least one RNA delivery molecule and at least one chimeric RNAi molecule according to the invention, wherein the chimeric RNAi molecule comprises double-stranded RNA comprising annealed complementary strands, one of which has a nucleotide sequence which is complementary to at least part of a target nucleotide sequence of a target gene of a pest species to be down-regulated and at least one carrier, excipient suitable for pharmaceutical use or for veterinary use, respectively.
The composition may be a composition suitable for topical use, such as application on the skin of an animal or human, for example as liquid compositions to be applied to the skin as drops, or by brushing, or a spray, also creams, ointments, etc. for topical application and transdermal patches.
Other conventional pharmaceutical dosage forms may also be produced, including tablets, capsules, pessiaries, suppositories, etc. The chosen form will depend upon the nature of the pest species and hence the nature of the disease it is desired to treat.
Preferred examples of pest species causing infections in human and animal are fungi. Target human pathogenic and animal pathogenic fungi include, but are not limited to the following:
In humans: Candida spp., particularly Candida albicans; Dermatophytes, including Epidermophyton spp., Trichophyton spp., and Microsporum spp.; Aspergillus spp., particularly Aspergillus flavus, Aspergillus fumigatus, Aspergillus nidulans, Aspergillus niger, Aspergillus terreus group; Blastomyces dermatitidis; Coccidioides immitis; Crytococcus neoformans; Histoplasma capsulatum Var. capsulatum or Var. duboisii; Sporothrix schenckii; Fusarium spp.; Scopulariopsis brevicaulis; Fonsecaea spp.
In animals: Candida spp.; Microsporum spp., particularly Microsporum canis, Microsporum gypseum; Trichophyton mentagrophytes; Apergillus spp.; Cryptococcus neoformans.
The composition may be a composition suitable for agronomical use, such as a spray, a coating, a powder and the like. In particular, the present invention provides pesticidal composition developed to be used in agriculture or horticulture. These pesticidal compositions may be prepared in a manner known per se. For example, the active compounds can be converted into the customary formulations, such as solutions, emulsions, wettable powders, water dispersible granules, suspensions, powders, dusting agents, foaming agents, pastes, soluble powders, granules, suspo-emulsion concentrates, microcapsules, fumigants, natural and synthetic materials impregnated with active compound and very fine capsules and polymeric substances.
Furthermore, the pesticidal compositions according to the present invention may comprise a synergist. The RNA delivery molecule and/or chimeric RNAi molecules, constructs, nucleotide sequences, or compositions thereof according to the invention, as such or in their formulations, can also be used in a mixture with known fungicides, bactericides, acaricides, nematicides or insecticides, to widen, for example, the activity spectrum or to prevent the development of resistance. In many cases, this results in synergistic effects, i.e. the activity of the mixture exceeds the activity of the individual components.
Additionally the RNA delivery molecule and/or chimeric RNAi molecules, constructs, nucleotide sequences or compositions thereof according to the invention, as such or in their formulations or above-mentioned mixtures, can also be used in a mixture with other known active compounds, such as herbicides, fertilizers and/or growth regulators.
The present invention also relates to fibrous pesticide composition and its use as pesticide, wherein the fibrous composition comprises a non-woven fiber and an effective amount of at least one of the RNA delivery molecule and/or chimeric RNAi molecules, nucleotide sequences, recombinant DNA constructs or compositions thereof described herein, covalently attached or stably adsorbed to the fiber.
In a further particular embodiment, the fiber is biodegradable and the adsorbed the RNA delivery molecule and/or chimeric RNAi molecules or compositions thereof as described herein, can be slowly released into a localized area of the environment to control pests in that area over a period of time.
The present invention also encompasses solid formulations of slow-release pesticidal composition comprising the molecules or constructs as described herein, and their use as pesticide. The formulations release the RNA delivery molecules and/or the chimeric RNAi molecule as described herein (a) into the environment (soil, aqueous medium, plants) in a controlled and slow fashion (complete release within several days up to a few months).
The present invention also relates to surfactant-diatomaceous earth compositions for pesticidal use in the form of dry spreadable granules comprising at least one RNA delivery molecule and/or at least one chimeric RNAi molecule as described herein. The granules comprises in addition to the diatomaceous earth, a surfactant composition designed to provide binding, rewetting and disintegration properties to the granules. By diatomaceous earth is meant a silica material characterized by a large surface area per unit volume. Diatomaceous earth is a naturally occurring material and consists mainly of accumulated shells or frustules of intricately structured amorphous hydrous silica secreted by diatoms.
The present invention also provides solid, water-insoluble lipospheres and their use as pesticide, wherein said lipospheres are formed of a solid hydrophobic core having a layer of a phospholipid embedded on the surface of the core, containing at least one RNA delivery molecule and/or chimeric RNAi molecule as described herein in the core, in the phospholipid, adhered to the phospholipid, or a combination thereof.
The pesticidal compound containing lipospheres have several advantages including stability, low cost of reagents, ease of manufacture, high dispersibility in an aqueous medium, a release rate for the entrapped compound that is controlled by the phospholipid coating and the carrier.
The invention further relates to pesticidal formulations in the form of microcapsules having a capsule wall made from a urea/dialdehyde precondensate and comprising at least one RNA delivery molecule and/or chimeric RNAi molecule as described herein.
In another specific embodiment, the composition may be a coating that can be applied to a substrate in order to protect said substrate from infestation by a pest species, such as a fungus and/or to prevent, arrest or reduce growth of the pest species on the substrate and thereby prevent damage caused by said pest species. In this embodiment, the composition can be used to protect any substrate or material that is susceptible to infestation by or damage caused by a pest species, for example foodstuffs and other perishable materials, and substrates such as wood. Preferred target pest species for this embodiment is are fungus species, including, but are not limited to, the following: Stachybotrys spp.; Apergillus spp.; Alternaria spp.; Cladosporium spp.
In this embodiment the composition will comprise at least one RNA delivery molecule and at least one chimeric RNAi molecule according to the invention, wherein the chimeric RNAi molecule comprises double-stranded RNA comprising annealed complementary strands, one of which has a nucleotide sequence which is complementary to at least part of a target nucleotide sequence of a target gene of the pest species to be down-regulated and optionally at least one carrier, excipient suitable for the intended use.
The nature of the excipients and the physical form of the composition may vary depending upon the nature of the substrate that it is desired to treat. For example, the composition may be a liquid that is brushed or sprayed onto or imprinted into the material or substrate to be treated, or a coating that is applied to the material or substrate to be treated.
The present invention further encompasses a method for treating and/or preventing fungal infestation on a substrate comprising applying an effective amount of any of the compositions described herein to said substrate.
The present invention also relates to methods for treating and/or preventing pest infestation on a substrate comprising applying an effective amount of a RNA delivery molecule and/or a chimeric RNAi molecule, nucleic acid, vector, or a composition thereof as described herein to said substrate.
The present invention also relates to methods for treating and/or preventing pest growth and/or pest infestation of a plant or propagative or reproductive material of a plant comprising applying an effective amount of a RNA delivery molecule and/or a chimeric RNAi molecule, nucleic acid, vector, or a composition thereof as described herein to a plant or to propagation or reproductive material of a plant.
In another embodiment, the invention relates to a method for controlling pest growth on a cell or an organism or for preventing pest infestation of a cell or an organism susceptible to infection to said pest species, comprising contacting said pest species with any of the RNA delivery molecule and/or the chimeric RNAi molecule, nucleic acid, vector, or a composition thereof described herein, whereby the dsRNA is taken up by said pest species and thereby controls growth or prevents infestation.
Bacteria can be engineered to produce any of the dsRNA or dsRNA constructs of the invention. These bacteria can be eaten by the pest species. When taken up, the dsRNA can initiate an RNAi response, leading to the degradation of the target mRNA and weakening or killing of the feeding pest.
Therefore, in a more specific embodiment, said RNA delivery molecule and/or the chimeric RNAi molecule is expressed by a prokaryotic, such as a bacterial, or eukaryotic, such as a yeast, host cell or host organism.
Some bacteria have a very close interaction with the host plant, such as symbiotic Rhizobium with the Leguminosea (for example Soy). Such recombinant bacteria could be mixed with the seeds (ie coating) and used as soil improvers. Alternatively, dsRNA producing bacteria can be sprayed directly onto the crops, for instance Bacillus thuringiensis species. Possible applications include intensive greenhouse cultures, for instance crops that are less interesting from a GMO point of view, as well as broader field crops such as soy.
This approach has several advantages, eg: since the problem of possible dicing by a plant host is not present, it allows the delivery of dsRNA into the gut lumen of the feeding pest; the use of bacteria as insecticides does not involve the generation of transgenic crops, especially for certain crops where transgenic variants are difficult to obtain; there is a broad and flexible application in that different crops can be simultaneously treated on the same field and/or different pests can be simultaneously targeted, for instance by combining different bacteria producing distinct dsRNAs.
According to another specific embodiment, the invention encompasses the GMO approaches and thus relates to a method as described above wherein said double-stranded RNA is expressed by said cell or organism infested with or susceptible to infestation by said pest species, for instance said cell is a plant cell or said organism is a plant.
The invention further relates to a method for increasing plant yield comprising introducing in a plant any of the RNA delivery molecule and/or chimeric RNAi molecule, nucleic acid, vector or composition thereof in an expressible format.
It should be understood that in the above described compositions and kits of the invention comprising both an RNA delivery molecule and a chimeric RNAi molecule, the sequences of the molecules should be such that the RNA binding protein or RNA-binding domain in the RNA delivery molecule recognizes and binds to the RNA recognition site, specific for the RNA binding protein or RNA-binding domain, in the chimeric RNAi molecule.
The invention will be further understood with reference to the following non-limiting examples.
The practice of the present invention will employ, unless otherwise indicated, conventional techniques used in recombinant DNA technology, molecular biology, biological testing, and the like, which are within the skill of the art. Such techniques are explained fully in the literature.
In Example 1, several constructs for RNA delivery molecules are described including possible ways for making them. In Example 2, several constructs for chimeric RNAi molecules are described. It should be clear that the present invention is not limited to the specific constructs exemplified herein.
The RNA delivery vehicle consists of a targeting protein such as transferrin of the target species fused to an RNA binding protein such as MS2, Nun or licT. The organization of the RNA delivery vehicles is: HIS-RNA-binding protein/domain-linker-transferrin.
Genbank accession numbers:
Step 1: To obtain the Nun gene sequence, PCR is performed with primers pR11 and pR12 on bacteriophage λ DNA and the PCR product is cloned into the TOPO TA Cloning® vector (Invitrogen) and sequence verified.
To obtain this fusion construct the same cloning steps are performed as in Example 1.1, but in Step 2 PCR primer pR14 is replaced by PCR primer pR18.
To obtain this fusion construct the same cloning steps are performed as in Example 1.1, but in Step 2 PCR primer pR13 is replaced by PCR primer pR15 and pR14 is replaced by PCR primer pR18.
To obtain this fusion construct the same cloning steps are performed as in Example 1.1, but in Step 2 PCR primer pR13 is replaced by PCR primer pR17 and pR14 is replaced by PCR primer pR18.
Step 1: To obtain the LicT gene sequence, PCR is performed with primers pR21 and pR22 on Bacillus subtilis DNA and the PCR product is cloned into the TOPO TA Cloning® vector and sequence verified.
To obtain this fusion construct the same cloning steps are performed as in Example 1.6, but in Step 2 PCR primer pR24 is replaced by PCR primer pR26.
Drosophila melanogaster contains two transferrin homologs, Tsf1 and Tsf2. Both Drosophila melanogaster transferrin homologs are fused to the full-length LicT protein or to its N-terminal dsRNA-binding domain following the same strategies as in Examples 1.6 and 1.7, but replacing the human transferrin-specific sequence of the primers pE11 through pE14 with Drosophila melanogaster transferrin-specific sequence.
Step 1: To obtain the MS2 gene sequence, PCR is performed with primers pR31 and pR32 on bacteriophage MS2 DNA and the PCR product is cloned into the TOPO TA Cloning® vector and sequence verified.
Drosophila melanogaster contains two transferrin homologs, Tsf1 and Tsf2. Both Drosophila melanogaster transferrin homologs are fused to the MS2 coat protein protein following the same strategies as in Example 1.9, but replacing the human transferrin-specific sequence of the primers pE11 through pE14 with Drosophila melanogaster transferrin-specific sequence.
1.11. Full-Length Nun Protein Linked to Galanthus nivalis Agglutinin
Step 1 and Step 2 are identical to Step 1 and Step 2 of Example 1.1.
Step 3: To obtain the Galanthus nivalis agglutinin sequence, PCR is performed with primers pE21 and pE22 on a Galanthus nivalis (Common Snowdrop) cDNA library and the PCR product is cloned into the TOPO TA Cloning® vector and sequence verified.
To obtain this fusion construct the same cloning steps are performed as in Example 1.11, but in Step 2 PCR primer pR14 is replaced by PCR primer pR18.
To obtain this fusion construct the same cloning steps are performed as in Example 1.11, but in Step 2 PCR primer pR13 is replaced by PCR primer pR15 and pR14 is replaced by PCR primer pR18.
To obtain this fusion construct the same cloning steps are performed as in Example 1.11, but in Step 2 PCR primer pR13 is replaced by PCR primer pR17 and pR14 is replaced by PCR primer pR18.
To obtain this fusion construct the same cloning steps are performed as in Example 1.15, but in Step 2 PCR primer pR24 is replaced by PCR primer pR26.
Step 1 and Step 2 are identical to Step 1 and Step 2 of Example 1.9.
Step 3 and Step 4 are identical to Step 3 and Step 4 of Example 1.11.
Step 1 and Step 2 are identical to Step 1 and Step 2 of Example 1.1.
Step 3: To obtain the Potato Leafroll virus capsid protein genomic sequence, PCR is performed with primers pE31 and pE32 on Potato Leafroll virus cDNA and the PCR product is cloned into the TOPO TA Cloning® vector and sequence verified.
To obtain this fusion construct the same cloning steps are performed as in Example 1.18, but in Step 2 PCR primer pR14 is replaced by PCR primer pR18.
To obtain this fusion construct the same cloning steps are performed as in Example 1.18, but in Step 2 PCR primer pR13 is replaced by PCR primer pR15 and pR14 is replaced by PCR primer pR18.
To obtain this fusion construct the same cloning steps are performed as in Example 1.18, but in Step 2 PCR primer pR13 is replaced by PCR primer pR17 and pR14 is replaced by PCR primer pR18.
Potato Leafroll virus read-through protein is fused to the full-length Nun protein or to either of the Nun dsRNA-binding domain fragments following the same strategies as in Examples 1.18 through 1.21, but in Step 3 PCR primer pE32 is replaced by PCR primer pE36 and in Step 4 PCR primer pE34 is replaced by PCR primer pE38.
Step 1 and Step 2 are identical to Step 1 and Step 2 of Example 1.6.
Step 3 and Step 4 are identical to Step 3 and Step 4 of Example 1.18.
To obtain this fusion construct the same cloning steps are performed as in Example 1.23, but in Step 2 PCR primer pR24 is replaced by PCR primer pR26.
Potato Leafroll virus read-through protein is fused to the full-length LicT protein or to its N-terminal dsRNA-binding domain following the same strategies as in Examples 1.23 and 1.24, but in Step 3 PCR primer pE32 is replaced by PCR primer pE36 and in Step 4 PCR primer pE34 is replaced by PCR primer pE38.
Step 1 and Step 2 are identical to Step 1 and Step 2 of Example 1.9.
Step 3 and Step 4 are identical to Step 3 and Step 4 of Example 1.18.
Potato Leafroll virus read-through protein is fused to the full-length MS2 protein following the same strategies as in Example 2.26, but in Step 3 PCR primer pE32 is replaced by PCR primer pE36 and in Step 4 PCR primer pE34 is replaced by PCR primer pE38.
The chimeric RNAi molecule is principally a hairpin construct that contains at least one target RNA sequence and, in the loop(s) or at the 3′ or 5′ end, at least one recognition sequence for an RNA-binding protein, such as for instance MS2, Nun or licT.
Target genes from the target species are cloned accordingly. Examples of target genes in C. elegans include 6-tubulin (Genbank accession NM—066966), sup-35 (Genbank accession number X73845) unc-22 (Genbank accession Z73899) and 60S ribosomal protein L9 (Genbank accession NM—066259), see Table 7. The length of the tested target RNA sequence is 80-450 base pairs.
Diabrotica virgifera, Meloidogyne incognita, and Magnaporthe grisea.
Nilaparvata lugens
C. elegans
M. incognita
Diabrotica virgifera
M. grisae
Promoters useful for the expression of dsRNA are a promoter from an RNA Poll, an RNA PollI, an RNA PollII, T7 RNA polymerase or SP6 RNA polymerase.
Several non-limiting constructs of chimeric RNAi molecules according to the invention are exemplified in
In the following example, several assays are described which are used to follow efficacy of RNAi in pest species.
The RNA vehicle complex principally consists of an RNAi mediating molecule (dsRNA or hairpin as described in example 2) to induce RNAi in the target organism and an RNA delivery vehicle (as described in example 1) to increase the efficiency of endo- and/or transcytosis.
RNA delivery vehicles, as described in Example 1, are produced in insect Sf9 cells after transfection with recombinant baculoviruses using the Bac-to-Bac® Baculovirus Expression System (Invitrogen). The His-tagged RNA delivery vehicles are protein purified over a HiTrap™ Chelating HP nickel column (Amersham Boisciences). The His-tag is removed by cleavage with recombinant TEV protease (Invitrogen). Protein purification with nickel-chelating resin and rTEV cleavage are also used when RNA delivery vehicle protein is obtained after expression in bacteria or the yeast Pichia Pastoris.
The RNAi mediating molecule is obtained using T7 polymerase transcription of the template DNA following the provided protocol of RNA dsRNA kit manufacturers (e.g. T7 RiboMAX™ Express RNAi System, Promega or obtained by Megascript RNAi™ kit, Ambion)
B) Administration of RNA Vehicle Complex (RVC) to C. elegans
The RVC complex can be delivered to the C. elegans gut by feeding on agar plates, soaking in liquid medium or injection into the gut lumen.
RVC Delivery into C. elegans by Soaking and Injection
RNAi is induced by injection of dsRNA into C. elegans or by feeding C. elegans a solution with dsRNA, called soaking (Gonczy P, Echeverri C, Oegema K, Coulson A, Jones S J, Copley R R, Duperon J, Oegema J, Brehm M, Cassin E, Hannak E, Kirkham M, Pichler S, Flohrs K, Goessen A, Leidel S, Alleaume A M, Martin C, Ozlu N, Bork P, Hyman A A. Nature. 2000 408 page 331-6; Maeda I, Kohara Y, Yamamoto M, Sugimoto A. Curr Biol. 2001 11 page 171-6). These methods can also be used to induce RNAi by feeding with RVC. The RVC complex is prepared by mixing the RNA vehicle protein and the RNA construct in physiological buffer. This solution is either injected into the gut lumen of C. elegans or C. elegans is soaked in a solution containing the RVC complex In the latter case, the C. elegans would drink the RVC in the solution and consequently ingest it into the gut. A variation of this theme is to add the RVC solution on top of E. coli seeded agar plates on which C. elegans can feed.
RNAi by feeding is induced in C. elegans by feeding with E. coli, which expresses dsRNA against the target gene (Fraser A G, Kamath R S, Zipperlen P, Martinez-Campos M, Sohrmann M, Ahringer J. Nature. 2000 408 page 325-30). Similarly, E. coli is co-transformed with a vector expressing the chimeric RNAi molecule against the target gene and a vector expressing the RNA delivery vehicle. C. elegans feeds on these E. coli and ingests RNA and protein to form the RVC. Upon digestion of E. coli, the RVC is released into the gut lumen.
All three delivery methods provide the RVC complex to the apical gut surface. The vehicle binds to apical surface proteins that mediate receptor-mediated endocytosis or are endocytosed specifically. This binding greatly enhances absorption into the gut.
C) Measurement of Improved RNAi Effectiveness in C. elegans
The effectiveness of the RVC to induce RNAi is measured using a specific and visible movement phenotype, “twitcher”. Down-regulation by RNAi or mutations in the C. elegans gene unc-22, which encodes Twitchin, causes convulsive muscle contractions called “twichter” phenotype (Benian G M et al. 1989. Sequence of an unusually large protein implicated in regulation of myosin activity in C. elegans. Nature 342: 45-50). In this experiment the following test reagents are used:
The effectiveness of the RVC(RNA vehicle complex) to induce RNAi in the target pest such as corn root worm or planthopper is measured by its potential to increase insect mortality. The selected pest gene is an essential gene and it has been demonstrated that knock down by RNAi causes impaired viability or lethality. In this experiment the following test reagents are used:
Endo/transcystosis is monitored using labeled RNA and labeled vehicles. In this experiment the following test reagents are used:
The vehicle may accumulate on the apical surface, in the gut cell and potentially at the basolateral surface (in case the vehicle was transcytosed). Similarly, labeled RNA may be visible on the gut cell surface/in the gut cells. It is expected that the RNA delivered via the RVC complex is accumulated significantly higher on/in the gut than plein RNA proving the concept of improved endo/transcytosis via RVC.
Stability of the dsRNa Constructs of the Present Invention in Plant Cells
The stability of the expressed constructs are analyzed with quantitative real-time PCR to determine the quantity of the expressed construct of the invention present in the transgenic plant cell relative to the quantities present in control transgenic plants, expressing a control dsRNA construct. The method to monitor PCR in real-time is described previously and is based on Taqman probes or intercalating dyes (SYBR green).
The expressed dsRNA constructs are quantified relative towards a standard dilution series of the template. The results are normalized by using the quantitative PCR data of a set of housekeeping genes from the same samples (Vandesompele et al., Genome Biology 2002, 3:research0034.1-0034.11).
Plant transformation always requires co-transformation of the plant with a construct containing the RNA delivery vehicle and a construct containing the RNA mediating molecule. The constructs of the present invention are cloned behind the CaMV35S promoter, a root or leave specific promoter or a feeding site specific promoter in a binary vector suitable for plant transformation. The binary vectors are transferred to Agrobacterium rhizogenes by three-parental mating (e.g. by E. coli HB101 containing pRK2013 helper plasmid). The binary vectors are transferred from E. coli into Agrobacterium tumifaciens. Subsequently crops plants (such as tomato, soybean, cotton or Tobacco) are co-transformed with the constructs (one containing the RNA delivery vehicle and one containing the RNA mediating molecule) via Agrobacterium-mediated transformation. As a control, Agrobacterium without binary vector is used. (Example of a protocol for corn transformation: Frame B R, Shou H, Chikwamba R K, Zhang Z, Xiang C, Fonger T M, Pegg S E, Li B, Nettleton D S, Pei D, Wang K. (2002) Agrobacterium tumefaciens-mediated transformation of maize embryos using a standard binary vector system. Plant Physiol. 129 page 13-22.). (Example of a protocol for rice transformation: Breitler J C, Meynard D, Van Boxtel J, Royer M, Bonnot F, Cambillau L, Guiderdoni E. (2004). A novel two T-DNA binary vector allows efficient generation of marker-free transgenic plants in three elite cultivars of rice (Oryza sativa L.). Transgenic Res 13:271-87).
Plant tissues are transformed with the constructs of the present invention and then regenerated into whole plants. Whole-transgenic plants are infested with corn rootworm eggs. Three parameters are scored: (1) Insect mortality, by which after various time points insects are collected and examined for stage of development and mortality compared to non-transformed plants and insecticide treated plants. (2) Plant-resistance, by which the quality of the roots are examined with a rating system such as nodes destroyed, roots pruned or undamaged roots. (3) Plant health, by which plant growth and root density of transformed versus non-transformed versus nematicide treated plants are compared. (A protocol describing the steps from shot gun mediated corn transformation to corn root worm resistance measurement can be found in Moellenbeck D J, Peters M L, Bing J W, Rouse J R, Higgins L S, Sims L, Nevshemal T, Marshall L, Ellis R T, Bystrak P G, Lang B A, Stewart J L, Kouba K, Sondag V, Gustafson V, Nour K, Xu D, Swenson J, Zhang J, Czapla T, Schwab G, Jayne S, Stockhoff B A, Narva K, Schnepf H E, Stelman S J, Poutre C, Koziel M, Duck N. (2001). Insecticidal proteins from Bacillus thuringiensis protect corn from corn rootworms. Nat. Biotechnol. 19 page 668-72.)
Plants (or plant) tissues are transformed with the constructs of the present invention and then regenerated into whole plants. Whole-transgenic plants are infested with plant hopper neonates, third instar nymphs or adults. Three parameters are scored: (1) Insect mortality, by which after various time points insects are collected and examined for stage of development and mortality compared to non-transformed plants and insecticide treated plants. (2) Plant-resistance, by which the quality of the rice stem and rice leaves are examined with a rating system such as rice stem/leaves have severe feeding damage, rice stem/leaves have limited feeding damage or undamaged steem/leaves. (3) Plant health, by which plant growth, steem length and leaf quality of transformed versus non-transformed versus nematicide treated plants are compared (a protocol describing the steps from rice transformation to plant hopper bio assay can be found in (Nayak P, Basu D, Das S, Basu A, Ghosh D, Ramakrishnan N A, Ghosh M, Sen S K. (1997). Proc Natl Acad Sci USA. 94:2111-6).
| Number | Date | Country | Kind |
|---|---|---|---|
| 04447234.8 | Oct 2004 | EP | regional |
| 04447252.0 | Nov 2004 | EP | regional |
This application is a divisional application from U.S. non-provisional application Ser. No. 11/666,017 which was a national stage filing under 35 under 35 U.S.C. 371 of international application PCT/EP2005/011441, filed Oct. 25, 2005, which was published under PCT Article 21(2) in English, and claims priority under 35 U.S.C. 119(e) to U.S. provisional application 60/621,718, filed Oct. 25, 2004, and to U.S. provisional application 60/621,718, filed Oct. 24, 2004 and to U.S. provisional application 60/628,976, filed Nov. 18, 2004, the disclosures of which are incorporated herein by reference.
| Number | Date | Country | |
|---|---|---|---|
| Parent | 11666017 | Apr 2007 | US |
| Child | 14284556 | US |
