Patent Application
20150133523
A Sequence Listing is contained in the file named “12778278”, which is 1153 kilobytes and was filed with U.S. application Ser. No. 12/778,278, filed May 12, 2010, which is a divisional of U.S. application Ser. No. 11/396,926, filed Apr. 3, 2006, which is a continuation-in-part of PCT/IB2005/003495, filed Oct. 4, 2005, which claims the benefit under 35 U.S.C. §119(e) of U.S. provisional application 60/615,695, filed Oct. 4, 2004; for which this application claims the benefit thereof. The Sequence Listing is attached and filed herewith and is incorporated herein by reference.
The invention relates to methods for controlling fungal growth on cells or organisms, methods for preventing fungal infestation of cells or organism and methods for down-regulating gene expression in fungi using double-stranded RNA. The invention also relates to transgenic plants resistant to fungal infestation.
RNA interference or “RNAi” is a process of sequence-specific down-regulation of gene expression (also referred to as “gene silencing” or “RNA-mediated gene silencing”) initiated by double-stranded RNA (dsRNA) that is complementary in sequence to a region of the target gene to be down-regulated (Fire, A. Trends Genet. Vol. 15, 358-363, 1999; Sharp, P. A. Genes Dev. Vol. 15, 485-490, 2001).
Over the last few years, down-regulation of target genes in multicellular organisms by means of RNA interference (RNAi) has become a well established technique. In general, RNAi comprises contacting the organism with a double-stranded RNA fragment (generally either as two annealed complementary single-strands of RNA or as a hairpin construct) having a sequence that corresponds to at least part of a gene to be down-regulated (the “target gene”). Reference may be made to International application WO 99/32619 (Carnegie Institute of Washington), International application WO 99/53050 (Benitec), and to Fire et al., Nature, Vol. 391, pp.806-811, February 1998 for general description of the RNAi technique.
In nematodes, RNAi can be performed by feeding the nematode with the RNAi fragment or with a bacterial strain that either contains the RNAi fragment or that upon ingestion by the nematode is capable of expressing the RNAi fragment. For a description of this so-called “RNAi by feeding”, reference may be made to International application WO 00/01846 by the present applicant, to 1998 East Coast Worm Meeting abstract 180—Timmons and Fire (see www.elegans.swmed.edu/wli/[ecwm98p180]/), and again to WO 99/32619.
RNAi has also been proposed as a means of protecting plants against plant parasitic nematodes, i.e. by expressing in the plant (e.g. in the entire plant, or in a part, tissue or cell of a plant) one or more nucleotide sequences that form a dsRNA fragment that corresponds to a target gene in the plant parasitic nematode that is essential for its growth, reproduction and/or survival. Reference may be made to U.S. Pat. No. 6,506,559 (based on WO 99/32619), column 11, line 55 to column 12, line 9 and column 13, line 61 to column 14, line 11), International application WO 00/01846 by the present applicant, page 7, lines 11-8, and International applications WO 01/96584, WO 01/37654 and WO 03/052110 for a description of such techniques.
Elbashir et al. (Nature, 411, 494-498, 2001) have demonstrated effective RNAi-mediated gene silencing in mammalian cells using dsRNA fragments of 21 nucleotides in length (also termed small interfering RNAs or siRNAs). These short siRNAs demonstrate effective and specific gene silencing, whilst avoiding the interferon-mediated non-specific reduction in gene expression which has been observed with the use of dsRNAs greater than 30 bp in length in mammalian cells (Stark G. R. et al., Ann Rev Biochem. 1998, 67: 227-264; Manche, L et al., Mol Cell Biol., 1992, 12: 5238-5248). Thus, RNAi has been proposed as an alternative to the use of antisense technology for specific down-regulation or gene silencing of target genes in mammalian cells.
Although the technique of RNAi has been generally known in the art in plants, nematodes and mammalian cells for some years, to date little is known about the use of RNAi to down-regulate gene expression in fungi.
Kadotani et al., (2003) Mol Plant Microbe Interac. 16: 769-776 describe RNA-mediated gene silencing in the ascomycete fungus Magnaporthe oryzae (formerly Magnaporthe grisea; anamorph Pyricularia oryzae Cav. and Pyricularia grisae), the causal agent of rice blast disease, by a mechanism having molecular features consistent with RNAi. Gene silencing was achieved by expression of dsRNA inside cells of the fungus: fungal protoplasts were transformed in the laboratory using DNA constructs capable of expressing the double-stranded RNA, such that the double-stranded RNA is transcribed within cells of the fungus.
Cogoni and Macino, (1999) Nature. 399: 166-169 describe gene silencing by RNAi in the filamentous fungus Neurospora crassa. Gene silencing was achieved by transforming fungal cells with a transgene capable of expressing the double-stranded RNA, allowing the double-stranded RNA to be transcribed within cells of the fungus.
Liu et al., (2002) Genetics. 160: 463-470 describe RNA interference in the human pathogenic fungus Cryptococcus neoformans. Again, RNAi was achieved by transforming fungal cells in culture with a DNA construct encoding the double-stranded RNA, such that the double-stranded RNA was transcribed in situ in the fungal cells.
These studies confirm that RNA interference pathways are active in a number of different species of fungi. However, to date RNAi has only been achieved in fungi by transcription of dsRNA within cells of the fungus, following transformation of fungal cells with a DNA construct or transgene from which the appropriate dsRNA may be transcribed.
RNAi techniques requiring transformation of fungal cells with a DNA construct that directs production of dsRNA within the fungal cells are useful for experimental studies within the laboratory but are clearly not suitable for many potential practical applications of RNAi, for example applications which require dsRNA to be introduced into many fungal cells on a large scale or in the field, for example, to protect plants against plant pathogenic fungi or large scale treatment of substrates to protect against fungal infestation, or for pharmaceutical or veterinary use in the treatment or prevention of fungal infestation in humans or animals.
It has now been found by the present inventors that gene expression can be specifically down-regulated in fungi by contacting intact fungal cells (i.e. with an intact cell wall) with double-stranded RNA outside the cell (i.e. external to the cell wall), wherein the double-stranded RNA comprises annealed complementary strands, one of which has a nucleotide sequence which corresponds to (i.e. is complementary to at least part of) a target nucleotide sequence of a target gene of a fungus to be down-regulated.
It has surprisingly been found that when intact fungal cells are contacted with double-stranded RNA outside the cell wall, the double-stranded RNA is taken up by the fungal cells in amounts sufficient to specifically cause inhibition of growth. This approach to RNAi in fungi avoids the need for complicated transformation procedures in order to introduce a transgene capable of directing expression of double-stranded RNA within cells of the fungus. Accordingly, there is no need for the fungus itself to be genetically manipulated and in particular no need to transform the fungal cells using non-natural procedures in order to introduce a DNA construct directing expression of dsRNA within the fungal cells. Hence, the technique is simple and of great practical utility and opens up a whole range of different applications of RNAi in fungi that simply would not be practical using the prior art techniques.
The methods of the invention can find practical application in any area of technology where it is desirable to inhibit viability, growth, development or reproduction of the fungus, or to decrease pathogenicity or infectivity of the fungus. The methods of the invention further find practical application where it is desirable to specifically down-regulate expression of one or more target genes in a fungus. Particularly useful practical applications include, but are not limited to, (1) protecting plants against plant pathogenic fungi; (2) pharmaceutical or veterinary use in humans and animals (for example to control, treat or prevent fungal infections in humans); (3) protecting materials against damage caused by fungi; (4) protecting perishable materials (such as foodstuffs, seed, etc.) against damage caused by fungi; (5) functional genomics in fungi to elucidate the gene function of fungal target genes and generally any application wherein fungi need to be controlled and/or wherein damage caused by fungi needs to be prevented.
In accordance with one embodiment the invention relates to a method for controlling fungal growth in or on a cell or an organism or for preventing fungal infestation of a cell or an organism susceptible to fungal infection, comprising contacting fungal cells with a double-stranded RNA from outside the fungal cell(s), wherein the double-stranded RNA comprises annealed complementary strands, one of which has a nucleotide sequence which is complementary to at least part of the nucleotide sequence of a fungal target gene, whereby the double-stranded RNA is taken up into the fungal cells and thereby controls growth or prevents infestation.
The expression “complementary to at least part of” as used herein means that the nucleotide sequence is fully complementary to the nucleotide sequence of the target over more than two nucleotides, for instance over at least 15, 16, 17, 18, 19, 20, 21, 22, 23 or 24 contiguous nucleotides.
According to a further embodiment, the invention relates to a method for down-regulating expression of a target gene in a fungus, comprising contacting fungal cell(s) with a double-stranded RNA from outside the fungal cell(s), wherein the double-stranded RNA comprises annealed complementary strands, one of which has a nucleotide sequence which is complementary to at least part of the nucleotide sequence of the fungal target gene to be down-regulated, whereby the double-stranded RNA is taken up into the fungal cells and thereby down-regulates expression of the fungal target gene.
According to one embodiment, the methods of the invention rely on uptake into fungal cells of double-stranded RNA present outside of the fungus (i.e. external to the cell wall) and does not require expression of double-stranded RNA within cells of the fungus. In addition, the present invention also encompasses methods as described above wherein the fungal cell(s) is contacted with a composition comprising the double-stranded RNA.
Said double-stranded RNA may be expressed by a prokaryotic (for instance but not limited to a bacterial) or eukaryotic (for instance but not limited to a yeast) host cell or host organism, or a symbiotic organism (e.g. green algae or cyanbacterium).
According to another embodiment, the methods of the invention rely on a GMO approach wherein the double-stranded RNA is expressed by a cell or an organism infested with or susceptible to infestation by fungi. Preferably, said cell is a plant cell or said organism is a plant.
Preferably, the present invention extends to methods as described herein, wherein said target gene comprises a sequence which is selected from the group comprising: (i) sequences which are at least 75%, at least 80% or 85% identical, preferably at least 90%, 95%, 96%, or more preferably at least 97%, 98% and still more preferably at least 99% identical to a sequence represented by any of SEQ ID NOs 3, 42, 99, 100, 527, 39, 60, 111, 112, 113, 114, 115, 116, 117, 536, 537, 538, 5, 43, 101, 102, 528, 1, 41, 97, 98, 526, 184, 185, 37, 59, 124, 9, 45, 106, 531, 188, 189, 13, 47, 109, 534, 33, 57, 126, 23, 52, 119, 35, 58, 127, 7, 44, 103, 104, 105, 529, 186, 187, 29, 55, 118, 17, 49, 108, 533, 25, 53, 121, 19, 50, 125, 31, 56, 123, 11, 46, 107, 532, 27, 54, 122, 21, 51, 120, 15, 48, 110, 535, 458, 486, 530, 460, 487, 539, 540, 462, 488, 541, 464, 489, 542, 466, 490, 543, 468, 491, 544, 470, 492, 545, 472, 493, 546, 474, 494, 547, 476, 496, 548, 478, 556, 549, 480, 497, 550, 482, 498, 551, 484, 499, 552 and 562 to 859, or the complement thereof, and (ii) sequences comprising at least 17, preferably at least 18, 19, 20 or 21, more preferably at least 22, 23 or 24 contiguous nucleotides of any of SEQ ID NOs 3, 42, 99, 100, 527, 39, 60, 111, 112, 113, 114, 115, 116, 117, 536, 537, 538, 5, 43, 101, 102, 528, 1, 41, 97, 98, 526, 184, 185, 37, 59, 124, 9, 45, 106, 531, 188, 189, 13, 47, 109, 534, 33, 57, 126, 23, 52, 119, 35, 58, 127, 7, 44, 103, 104, 105, 529, 186, 187, 29, 55, 118, 17, 49, 108, 533, 25, 53, 121, 19, 50, 125, 31, 56, 123, 11, 46, 107, 532, 27, 54, 122, 21, 51, 120, 15, 48, 110, 535, 458, 486, 530, 460, 487, 539, 540, 462, 488, 541, 464, 489, 542, 466, 490, 543, 468, 491, 544, 470, 492, 545, 472, 493, 546, 474, 494, 547, 476, 496, 548, 478, 556, 549, 480, 497, 550, 482, 498, 551, 484, 499, 552 and 562 to 859, or the complement thereof, or wherein said target gene is an orthologue of a gene comprising at least 17 contiguous nucleotides of any of SEQ ID NOs 3, 42, 99, 100, 527, 39, 60, 111, 112, 113, 114, 115, 116, 117, 536, 537, 538, 5, 43, 101, 102, 528, 1, 41, 97, 98, 526, 184, 185, 37, 59, 124, 9, 45, 106, 531, 188, 189, 13, 47, 109, 534, 33, 57, 126, 23, 52, 119, 35, 58, 127, 7, 44, 103, 104, 105, 529, 186, 187, 29, 55, 118, 17, 49, 108, 533, 25, 53, 121, 19, 50, 125, 31, 56, 123, 11, 46, 107, 532, 27, 54, 122, 21, 51, 120, 15, 48, 110, 535, 458, 486, 530, 460, 487, 539, 540, 462, 488, 541, 464, 489, 542, 466, 490, 543, 468, 491, 544, 470, 492, 545, 472, 493, 546, 474, 494, 547, 476, 496, 548, 478, 556, 549, 480, 497, 550, 482, 498, 551, 484, 499, 552 and 562 to 859, or the complement thereof.
The present invention thus also relates to a method for producing a plant resistant to a plant pathogenic fungus, comprising:
According to still other embodiments, in the methods of the invention, the double-stranded RNA is expressed from a recombinant construct, which construct comprises at least one regulatory sequence operably linked to said nucleotide sequence which is complementary to at least part of said nucleotide sequence of said fungal target gene to be down-regulated.
The fungal cell(s) can be any fungal cell, meaning any cell present within or derived from an organism belonging to the Kingdom Fungi. The methods of the invention are applicable to all fungi and fungal cells that are susceptible to gene silencing by RNA interference and that are capable of internalising double-stranded RNA from their immediate environment.
In one embodiment of the invention, the fungus may be a mould, or more particularly a filamentous fungus. In other embodiments of the invention, the fungus may be a yeast.
In one embodiment the fungus may be an ascomycetes fungus, i.e. a fungus belonging to the Phylum Ascomycota.
In preferred, but non-limiting, embodiments of the invention the fungal cell is chosen from the group consisting of:
(1) a fungal cell of, or a cell derived from a plant pathogenic fungus, such as but not limited to Acremoniella spp., Alternaria spp. (e.g. Alternaria brassicola or Alternaria solani), Ascochyta spp. (e.g. Ascochyta pisi), Botrytis spp. (e.g. Botrytis cinerea or Botryotinia fuckeliana), Cladosporium spp., Cercospora spp. (e.g. Cercospora kikuchii or Cercospora zaea-maydis), Cladosporium spp. (e.g. Cladosporium fulvum), Colletotrichum spp. (e.g. Colletotrichum lindemuthianum), Curvularia spp., Diplodia spp. (e.g. Diplodia maydis), Erysiphe spp. (e.g. Erysiphe graminis f.sp. graminis, Erysiphe graminis f.sp. hordei or Erysiphe pisi), Erwinia armylovora, Fusarium spp. (e.g. Fusarium nivale, Fusarium sporotrichioides, Fusarium oxysporum, Fusarium graminearum, Fusarium germinearum, Fusarium culmorum, Fusarium solani, Fusarium moniliforme or Fusarium roseum), Gaeumanomyces spp. (e.g. Gaeumanomyces graminis f.sp. Gibberella spp. (e.g. Gibberella zeae), Helminthosporium spp. (e.g. Helminthosporium turcicum, Helminthosporium carbonum, Helminthosporium mavdis or Helminthosporium sigmoideum), Leptosphaeria salvinii, Macrophomina spp. (e.g. Macrophomina phaseolina), Magnaportha spp. (e.g. Magnaporthe oryzae), Mycosphaerella spp., Nectria spp. (e.g. Nectria heamatococca), Peronospora spp. (e.g. Peronospora manshurica or Peronospora tabacina), Phoma spp. (e.g. Phoma betae), Phakopsora spp. (e.g. Phakopsora pachyrhizi), Phymatotrichum spp. (e.g. Phymatotrichum omnivorum), Phytophthora spp. (e.g. Phytophthora cinnamomi, Phytophthora cactorum, Phytophthora phaseoli, Phytophthora parasitica, Phytophthora citrophthora, Phytophthora megasperma f.sp. soiae or Phytophthora infestans), Plasmopara spp. (e.g. Plasmopara viticola), Podosphaera spp. (e.g. Podosphaera leucotricha), Puccinia spp. (e.g. Puccinia sorghi, Puccinia striiformis, Puccinia graminis f.sp. tritici, Puccinia asparagi, Puccinia recondita or Puccinia arachidis), Pythium spp. (e.g. Pythium aphanidermatum), Pyrenophora spp. (e.g. Pyrenophora tritici-repentens or Pyrenophora teres), Pyricularia spp. (e.g. Pyricularia oryzae), Pythium spp. (e.g. Pythium ultimum), Rhincosporium secalis, Rhizoctonia spp. (e.g. Rhizoctonia solani, Rhizoctonia oryzae or Rhizoctonia cerealis), Rhizopus spp. (e.g. Rhizopus chinensid), Scerotium spp. (e.g. Scerotium rolfsii), Sclerotinia spp. (e.g. Sclerotinia sclerotiorum), Septoria spp. (e.g. Septoria lycopersici, Septoria glycines, Septoria nodorum or Septoria Thielaviopsis spp. (e.g. Thielaviopsis basicola), Tilletia spp., Trichoderma spp. (e.g. Trichoderma virde), Uncinula spp. (e.g. Uncinula necator), Ustilago maydis (e.g. corn smut), Venturia spp. (e.g. Venturia inaequalis or Venturia pirina) or Verticillium spp. (e.g. Verticillium dahliae or Verticillium albo-atrum);
(2) a fungal cell of, or a cell derived from a fungus capable of infesting humans such as, but not limited to, 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 or Aspergillus terreus); Blastomyces dermatitidis; Paracoccidioides brasiliensis; Coccidioides immitis; Cryptococcus neoformans; Histoplasma capsulatum Var. capsulatum or Var. duboisii; Sporothrix schenckii; Fusarium spp.; Scopulariopsis brevicaulis; Fonsecaea spp.; Penicillium spp.; or Zygomycetes group of fungi (particularly Absidia corymbifera, Rhizomucor pusillus or Rhizopus arrhizus);
(3) a fungal cell of, or a cell derived from a fungus capable of infesting animals such as, but not limited to Candida spp., Microsporum spp. (particularly Microsporum canis or Microsporum gypseum), Trichophyton mentagrophytes, Aspergillus spp., or Cryptococcus neoforman;
and
(4) a fungal cell of, or a cell derived from a fungus that causes unwanted damage to substrates or materials, such as fungi that attack foodstuffs, seeds, wood, paint, plastic, clothing etc. Examples of such fungi are the moulds, including but not limited to Stachybotrys spp., Aspergillus spp., Alternaria spp., Cladosporium spp., Penicillium spp. or Phanerochaete chrysosporium.
Preferred plant pathogenic fungi according to the invention are Cercospora spp. (e.g. Cercospora kikuchii or Cercospora zaea-maydis) causing e.g. black and yellow sigatoka in banana; Colletotrichum spp. (e.g. Colletotrichum lindemuthianum) causing e.g. anthracnose in corn; Curvularia spp. causing seedling blight; Diplodia spp. (e.g. Diplodia maydis) causing e.g. ear, kernel and stalk rots in corn; Fusarium spp. (e.g. Fusarium nivale, Fusarium oxysporum, Fusarium graminearum, Fusarium germinearum, Fusarium culmorum, Fusarium solani, Fusarium moniliforme or Fusarium roseum) causing e.g. ear, kernel and stalk rots in corn, fusarium wilt in cotton and Panama disease in banana; Gibberella spp. causing e.g. ear, kernel and stalk rots in corn; Magnaportha spp. (e.g. Magnaporthe oryzae) causing rice blast; Mycosphaerella spp. causing e.g. black and yellow sigatoka in banana; Phakopsora spp. (e.g. Phakopsora pachyrhizi) causing e.g. soybean rust; Phytophthora spp.(e.g. Phytophthora cinnamomi, Phytophthora cactorum, Phytophthora phaseoli, Phytophthora parasitica, Phytophthora citrophthora, Phytophthora megasperma f.sp. soiae or Phytophthora infestans) causing e.g. late blight in potato and tomato; Puccinia spp. (e.g. Puccinia sorghi, Puccinia striiformis (yellow rust), Puccinia graminis f.sp. tritici, Puccinia asparagi, Puccinia recondita or Puccinia arachidis) causing e.g. common rust in corn; Rhizoctonia spp. (e.g. Rhizoctonia solani, Rhizoctonia oryzae or Rhizoctonia cerealis) causing e.g. sheath blight in rice or early blight in potato; Rhizopus spp. (e.g. Rhizopus chinensid) causing seedling blight; Trichoderma spp. (e.g. Trichoderma virde) causing seedling blight; or Verticillium spp. (e.g. Verticillium dahliae or Verticillium albo-atrum) causing e.g. verticillium wilt in cotton.
Particularly preferred plant pathogenic fungi according to the invention are Magnaporthe oryzae causing e.g. rice blast; Rhizoctonia spp. (e.g. Rhizoctonia solani, Rhizoctonia oryzae or Rhizoctonia cerealis) causing e.g. sheath blight in rice; Curvularia spp., Rhizopus spp. (e.g. Rhizopus chinensid), Trichoderma spp. (e.g. Trichoderma virde) causing seedling blight in rice; Phakopsora spp. causing e.g. soybean rust; Phytophthora spp. (e.g. Phytophthora cinnamomi, Phytophthora cactorum, Phytophthora phaseoli, Phytophthora parasitica, Phytophthora citrophthora, Phytophthora megasperma f.sp. soiae or Phytophthora infestans) causing e.g. late blight in tomato and potato; Cercospora spp. (e.g. Cercospora kikuchii or Cercospora zaea-maydis) or Mycosphaerella spp. causing e.g. black and yellow sigatoka in banana; or Fusarium spp. (e.g. Fusarium nivale, Fusarium oxysporum, Fusarium graminearum, Fusarium germinearum, Fusarium culmorum, Fusarium solani, Fusarium moniliforme or Fusarium roseum) causing e.g. Panama disease in banana.
A particularly preferred plant pathogenic fungus is Magnaporthe oryzae causing rice blast.
The fungal cell may be an intact fungal cell, meaning that the fungal cell has a cell wall. In this non-limiting embodiment, the fungal cell is contacted with double-stranded RNA by contacting the intact fungal cell with the double-stranded RNA. The cell wall of the fungal cell need not be removed prior to contact with the double-stranded RNA. Thus, when the fungal cell has a cell wall, the method of the invention comprises contacting the fungal cell with at least one double-stranded RNA, wherein the dsRNA is added or contacted outside of the fungal cell and external to the cell wall of the fungal cell, wherein the double-stranded RNA comprises annealed complementary strands, one of which has a nucleotide sequence which corresponds to a target nucleotide sequence of a target fungal gene to be down-regulated. The dsRNA is taken up by the fungal cell(s) through the cell wall.
The term “fungal cell” encompasses fungal cells of all types and at all stages of development, including specialised reproductive cells such as sexual and asexual spores. As used herein the fungal cell encompasses the fungus as such and also other life forms of the fungus, such as haustoria, conidia, mycelium, penetration peg, spore, zoospores etc.
In cases where fungi reproduce both sexually and asexually, these fungi have two names: the teleomorph name describes the fungus when reproducing sexually; the anamorph name refers to the fungus when reproducing asexually. The holomorph name refers to the “whole fungus”, encompassing both reproduction methods. When referring to one of these names in this invention, the “whole” fungus is referred to.
According to one embodiment of the present invention, the fungal cell which is contacted with the dsRNA is a plant pathogenic fungal cell in a life stage outside a plant cell, for example in the form of a hypha, germ tube, appressorium, conidium (asexual spore), ascocarp, cleistothecium, or ascospore (sexual spore outside the plant).
According to another embodiment of the present invention, the fungal cell which is contacted with the dsRNA is a plant pathogenic fungal cell in a life stage inside a plant cell, for example a pathogenic form such as a penetration peg, a hypha, a spore or a haustorium.
The present invention relates to any gene of interest in the fungus (which may be referred to herein as the “target gene”) that can be down-regulated. These can be coding or non-coding genes.
The terms “down-regulation of gene expression” and “inhibition of gene expression” are used interchangeably and refer to a measurable or observable reduction in gene expression or a complete abolition of detectable gene expression, at the level of protein product and/or mRNA product from the target gene, or at the level of phenotype. Down-regulation or inhibition of gene expression is “specific” when down-regulation or inhibition of the target gene occurs without manifest effects on other genes of the fungal cell. The down-regulation effect of the dsRNA on gene expression may be calculated as being at least 30%, 40%, 50%, 60%, preferably 70%, 80% or even more preferably 90% or 95% when compared with normal gene expression.
Depending on the nature of the target gene, down-regulation or inhibition of gene expression in cells of a fungus can be confirmed by phenotypic analysis of the cell or the whole fungus or by measurement of mRNA or protein expression using molecular techniques such as RNA solution hybridization, PCR, nuclease protection, Northern hybridization, reverse transcription, gene expression monitoring with a microarray, antibody binding, enzyme linked immunosorbent assay (ELISA), Western blotting, radioimmunoassay (RIA), other immunoassays, or fluorescence activated cell analysis (FACS).
The “target gene” may be essentially any gene that it is desirable to be inhibited because it interferes with growth or pathogenicity or infectivity of the fungus. For instance if the method of the invention is to be used to prevent fungal growth and/or infestation then it is preferred to select a target gene which is essential for viability, growth, development or reproduction of the fungus, or any gene that is involved with pathogenicity or infectivity of the fungus, such that specific inhibition of the target gene leads to a lethal phenotype or decreases or stops fungal infestation.
According to one non-limiting embodiment, the target gene is such that when its expression is down-regulated or inhibited using the method of the invention, the fungal cell is killed, or the reproduction or growth of the fungal cell is stopped or retarded. This type of target genes is considered to be essential for the viability of the fungus cell(s) and is referred to as essential genes. Therefore, the present invention encompasses a method as described herein, wherein the target gene is an essential gene.
Particular essential target genes suitable for the methods of the present invention, are genes involved in essential cellular functions that maintain cell viability, cell growth and development, and reproduction. Examples of still other suitable target genes involved in different cellular processes are described in Tables 1 and 2.
According to a further non-limiting embodiment, the target gene is such that when it is down-regulated using the method of the invention, the infestation or infection by the fungus, the damage caused by the fungus, and/or the ability of the fungus to infest or infect host organisms and/or cause such damage, is reduced. The terms “infest” and “infect” or “infestation” and “infection” are generally used interchangeably throughout. This type of target genes is considered to be involved in the pathogenicity or infectivity of the fungus. Therefore, the present invention extends to methods as described herein, wherein the target gene is involved in the pathogenicity or infectivity of the fungus, preferably the fungal target gene is involved in the formation of germ tubes, conidia attachment, formation of appressoria, formation of the penetration peg or formation of conidia. The advantage of choosing the latter type of target gene is that the fungus is blocked to infect further plants or plant parts and to form further generations. A further advantage of using a target gene involved in pathogenicity or infectivity is that the dsRNA can be taken up by the fungus when it is growing inside the plant, so that the spores formed are unable to infect further plant parts.
According to one embodiment, target genes are conserved genes or fungus-specific genes.
Some preferred, but non-limiting, examples of suitable target genes are listed in Tables 1 and 2.
The invention thus relates to RNAi-mediated down-regulation or inhibition of one or more of the Magnaporthe grisea target genes listed above in Table 1, and also to down-regulation of the homologous/orthologous target genes in other fungal species as listed in Table 2. Therefore, the present invention extends to methods as described herein wherein the fungal target gene is involved in any of the cellular functions as defined in Table 1 (rightmost column). A non-limiting example is for instance a method as described herein wherein the fungal target gene is a gene involved in the function of a ribosome, proteasome, spliceosome, APC complex; or a gene involved in nuclear transport, translation initiation, transcription (e.g. transcription activation), intracellular membrane traffic, DNA replication, mitotic spindle formation, vesicle transport or the cytoskeleton.
In addition, any suitable double-stranded RNA or nucleotide fragment capable of directing RNAi or RNA-mediated gene silencing or inhibition of a fungal target gene may be used in the methods of the invention.
In the methods of the present invention, dsRNA is used to inhibit growth or to interfere with the pathogenicity or infectivity of the fungus.
The invention thus relates to isolated 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 fungus. The target gene may be any of the target genes described herein, or a part thereof that exerts the same function. According to one embodiment of the present invention, an isolated double-stranded RNA is provided comprising annealed complementary strands, one of which has a nucleotide sequence which is complementary to at least part of a nucleotide sequence of a fungal target gene, wherein said fungal target gene is essential for the viability, growth, development or reproduction of the fungus, preferably said fungal target gene is involved in any of the cellular functions as defined in Table 1; or wherein said fungal target gene is involved in the pathogenicity or infectivity of the fungus, preferably said fungal target gene is involved in the formation of germ tubes, conidia attachment, formation of appressoria, formation of the penetration peg or formation of conidia, said nucleotide sequence being capable of inhibiting expression of the target gene. According to one embodiment the present invention relates to an isolated double-stranded RNA comprising annealed complementary strands, one of which has a nucleotide sequence which is complementary to at least part of a nucleotide sequence of a fungal target gene, wherein said target gene comprises a sequence which is selected from the group comprising: (i) sequences which are at least 75%%, at least 80% or 85% identical, preferably at least 90%, 95%, 96%, or more preferably at least 97%, 98% and still more preferably at least 99% identical to a sequence represented by any of SEQ ID NOs 3, 42, 99, 100, 527, 39, 60, 111, 112, 113, 114, 115, 116, 117, 536, 537, 538, 5, 43, 101, 102, 528, 1, 41, 97, 98, 526, 184, 185, 37, 59, 124, 9, 45, 106, 531, 188, 189, 13, 47, 109, 534, 33, 57, 126, 23, 52, 119, 35, 58, 127, 7, 44, 103, 104, 105, 529, 186, 187, 29, 55, 118, 17, 49, 108, 533, 25, 53, 121, 19, 50, 125, 31, 56, 123, 11, 46, 107, 532, 27, 54, 122, 21, 51, 120, 15, 48, 110, 535, 458, 486, 530, 460, 487, 539, 540, 462, 488, 541, 464, 489, 542, 466, 490, 543, 468, 491, 544, 470, 492, 545, 472, 493, 546, 474, 494, 547, 476, 496, 548, 478, 556, 549, 480, 497, 550, 482, 498, 551, 484, 499, 552 and 562 to 859 or the complement thereof, and (ii) sequences comprising at least 17, preferably at least 18, 19, 20 or 21, more preferably at least 22, 23 or 24 contiguous nucleotides of any of SEQ ID NOs 3, 42, 99, 100, 527, 39, 60, 111, 112, 113, 114, 115, 116, 117, 536, 537, 538, 5, 43, 101, 102, 528, 1, 41, 97, 98, 526, 184, 185, 37, 59, 124, 9, 45, 106, 531, 188, 189, 13, 47, 109, 534, 33, 57, 126, 23, 52, 119, 35, 58, 127, 7, 44, 103, 104, 105, 529, 186, 187, 29, 55, 118, 17, 49, 108, 533, 25, 53, 121, 19, 50, 125, 31, 56, 123, 11, 46, 107, 532, 27, 54, 122, 21, 51, 120, 15, 48, 110, 535, 458, 486, 530, 460, 487, 539, 540, 462, 488, 541, 464, 489, 542, 466, 490, 543, 468, 491, 544, 470, 492, 545, 472, 493, 546, 474, 494, 547, 476, 496, 548, 478, 556, 549, 480, 497, 550, 482, 498, 551, 484, 499, 552 and 562 to 859 or the complement, or wherein said target gene is an orthologue of a gene comprising at least 17 contiguous nucleotides of any of SEQ ID NOs 562 to 859, or the complement thereof.
Depending on the assay used to measure gene silencing, the growth inhibition can be quantified as being greater than about 5%, 10%, more preferably about 20%, 25%, 33%, 50%, 60%, 75%, 80%, most preferably about 90%, 95%, or about 99% as compared to a target cell that has been treated by control dsRNA.
According to another embodiment of the present invention, an isolated double-stranded RNA is provided, wherein at least one of said annealed complementary strands comprises the RNA equivalent of at least one of the nucleotide sequences represented by any of SEQ ID NOs 99, 100, 527, 111, 112, 113, 114, 115, 116, 117, 536, 537, 538, 101, 102, 528, 97, 98, 526, 124, 106, 531, 109, 534, 126, 119, 127, 103, 104, 105, 529, 118, 108, 533, 121, 125, 123, 107, 532, 122, 120, 110, 535, 530, 539, 540, 541, 542, 543, 544, 545, 546, 547, 548, 549, 550, 551, 552 and 562 to 859, or the RNA equivalent of a fragment of at least 17, preferably at least 18, 19, 20 or 21, more preferably at least 22, 23 or 24 basepairs in length thereof. Preferably said isolated double-stranded RNA comprises the RNA equivalent of at least one of the nucleotide sequences represented by any of SEQ ID NOs 192, 201, 202, 193, 190, 191, 196, 199, 200, 194, 195, 198 and 197, or a double-stranded fragment of 17, preferably at least 18, 19, 20 or 21, more preferably at least 22, 23 or 24 basepairs in length thereof. According to another embodiment of the present invention, an isolated double-stranded RNA is provided comprising annealed complementary strands, one of which has a nucleotide sequence which is complementary to at least part of a nucleotide sequence of a fungal target, for use as a medicament. According to another embodiment of the present invention the use as a medicament is provided for the isolated double-stranded RNA as described above.
If the method of the invention is used for controlling growth or infestation of fungus in or on a host cell or host organism, it is preferred that the double-stranded RNA does not share any significant homology with any host gene, or at least not 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 region. If genomic sequence data, preferentially transcriptome data, is available for the host organism one may cross-check sequence identity with the double-stranded RNA using standard bioinformatics tools. In one embodiment, there is no sequence identity between the dsRNA and a host sequences over 21 contiguous nucleotides, meaning that in this context, it is preferred that 21 contiguous base pairs of the dsRNA do not occur in the genome of the host organism. In another embodiment, there is less than about 10% or less than about 12.5 sequence identity over 24 contiguous nucleotides of the dsRNA with any nucleotide sequence from a host species.
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 able to base-pair with the first strand.
The expression “target region” or “target nucleotide sequence” of the target fungal gene may be any suitable region or nucleotide sequence of the gene. The target region should comprise at least 17, at least 18 or at least 19 consecutive nucleotides of the target gene, more preferably at least 20 or at least 21 nucleotide and still more preferably at least 22, 23 or 24 nucleotides of the target gene.
It is preferred that (at least part of) the double-stranded RNA will share 100% sequence identity with the target region of the fungal target gene. However, it will be appreciated that 100% sequence identity over the whole length of the double-stranded region 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 terms “corresponding to” or “complementary to” are used herein interchangeable, and when these terms are used to refer to sequence correspondence between the double-stranded RNA and the target region of the target gene, they are to be interpreted accordingly, i.e. as not absolutely requiring 100% sequence identity. However, the % sequence identity between the double-stranded RNA and the target region will generally be at least 80% or 85% identical, preferably at least 90%, 95%, 96%, or more preferably at least 97%, 98% and still more preferably at least 99% identical.
The term “complementary” as used herein relates to both DNA-DNA complementarity as to DNA-RNA complementarity. In analogy herewith, the term “RNA equivalent” substantially means that in the DNA sequence(s), the base “T” may be replaced by the corresponding base “U” normally present in ribonucleic acids.
Although the dsRNA contains a sequence which corresponds to the target region of the target gene 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 or inserted into the target-specific sequence, provided that such sequences do not affect performance of the dsRNA in RNA inhibition to a material extent.
The dsRNA may contain one or more substitute bases in order to optimise performance in RNAi. Substitution of even a single nucleotide may have an effect on activity of the dsRNA in RNAi. It will be apparent to the skilled reader how to vary each of the bases of the dsRNA in turn and test the activity of the resulting siRNAs (e.g. in a suitable in vitro test system) in order to optimise the performance of a given dsRNA.
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.
It has been previously reported that the formation of short interfering RNAs (siRNAs) of about 21 bp is desirable for effective gene silencing. However, in applications of applicant it has been shown that the minimum length of dsRNA preferably is at least about 80-100 bp in order to be efficiently taken up by certain pest organisms. There are indications that in invertebrates such as the free living nematode C. elegans or the plant parasitic nematode Meloidogyne incognita, these longer fragments are more effective in gene silencing, possibly due to a more efficient uptake of these long dsRNA by the invertebrate.
It has also recently been suggested that synthetic RNA duplexes consisting of either 27-mer blunt or short hairpin (sh) RNAs with 29 bp stems and 2-nt 3′ overhangs are more potent inducers of RNA interference than conventional 21-mer siRNAs. Thus, molecules based upon the targets identified above and being either 27-mer blunt or short hairpin (sh) RNA's with 29-bp stems and 2-nt 3′overhangs are also included within the scope of the invention.
Therefore, in one embodiment, the double-stranded RNA fragment (or region) will itself preferably be at least 17 bp in length, preferably 18 or 19bp in length, more preferably at least 20bp, more preferably at least 21 bp, or at least 22 bp, or at least 23 bp, or at least 24 bp, 25 bp, 26 bp or at least 27 bp in length. The expressions “double-stranded RNA fragment” or “double-stranded RNA region” refer to a small entity of the double-stranded RNA corresponding with (part of) the target gene.
Generally, the double-stranded RNA is preferably between about 17-1500 bp, even more preferably between about 80-1000 bp and most preferably between about 17-27 bp or between about 80-250 bp; such as double-stranded RNA regions of about 17 bp, 18 bp, 19 bp, 20 bp, 21 bp, 22 bp, 23 bp, 24 bp, 25 bp, 27 bp, 50 bp, 80 bp, 100 bp, 150 bp, 200 bp, 250 bp, 300 bp, 350 bp, 400 bp, 450 bp, 500 bp, 550 bp, 600 bp, 650 bp, 700 bp, 900 bp, 100 bp, 1100 bp, 1200 bp, 1300 bp, 1400 bp or 1500 bp.
The upper limit on the length of the double-stranded RNA may be dependent on i) the requirement for the dsRNA to be taken up by the fungal cell and ii) the requirement for the dsRNA to be processed within the cell into fragments that direct RNAi. The chosen length may also be influenced by the method of synthesis of the RNA and the mode of delivery of the RNA to the cell. Preferably the double-stranded RNA to be used in the methods of the invention will be less than 10,000 bp in length, more preferably 1000 bp or less more preferably 500 bp or less, more preferably 300 bp or less, more preferably 100 bp or less. For any given target gene and fungus, the optimum length of the dsRNA for effective inhibition may be determined by experiment.
The double-stranded RNA may be fully or partially double-stranded. Partially double-stranded RNAs may include short single-stranded overhangs at one or both ends of the double-stranded portion, provided that the RNA is still capable of being taken up by fungal cells and directing RNAi.
The methods of the invention can encompass simultaneous or sequential provision of two or more different double-stranded RNAs or RNA constructs to the same fungal cell, so as to achieve down-regulation or inhibition of multiple target genes or to achieve a more potent inhibition of a single target gene.
Alternatively, multiple targets are hit by the provision of one double-stranded RNA that hits multiple target sequences, and a single target is more efficiently inhibited by the presence of more than one copy of the double-stranded RNA fragment corresponding to the target gene. Thus, in one embodiment of the invention, the double-stranded RNA construct comprises multiple dsRNA regions, at least one strand of each dsRNA region comprising a nucleotide sequence that is complementary to at least part of a target nucleotide sequence of a fungal target gene. According to the invention, the dsRNA regions in the RNA construct may be complementary to the same or to different target genes and/or the dsRNA regions may be complementary to targets from the same or from different fungus species. Use of such dsRNA constructs in a plant host cell, thus establishes a more potent resistance to a single or to multiple fungal species in the plant.
The terms “hit”, “hits” and “hitting” are alternative wordings to indicate that at least one of the strands of the dsRNA is complementary to, and as such may bind to, the target gene or nucleotide sequence.
In one embodiment, the double-stranded RNA region comprises multiple copies of the nucleotide sequence that is complementary to the target gene. Alternatively, the dsRNA hits a further target sequence of the same target gene. The invention thus encompasses isolated double-stranded RNA constructs comprising at least two copies of said nucleotide sequence complementary to at least part of a nucleotide sequence of a fungal target. In another embodiment the invention relates to an isolated double-stranded RNA construct comprising at least two copies of the RNA equivalent of at least one of the nucleotide sequences represented by any of SEQ ID NOs 99, 100, 527, 111, 112, 113, 114, 115, 116, 117, 536, 537, 538, 101, 102, 528, 97, 98, 526, 124, 106, 531, 109, 534, 126, 119, 127, 103, 104, 105, 529, 118, 108, 533, 121, 125, 123, 107, 532, 122, 120, 110, 535, 530, 539, 540, 541, 542, 543, 544, 545, 546, 547, 548, 549, 550, 551, 552 and 562 to 859, or comprising at least two copies of the RNA equivalent of a fragment of at least 17 basepairs in length thereof, preferably at least 18, 19, 20 or 21, more preferably at least 22, 23 or 24 basepairs in length thereof.
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.
The expressions “a further target gene” or “at least one other target gene” mean for instance a second, a third or a fourth, etc. target gene.
DsRNA that hits more than one of the above-mentioned targets, or a combination of different dsRNA against different of the above mentioned targets may be developed or used in the methods of the present invention.
Accordingly the invention relates to an isolated double-stranded RNA construct comprising at least two copies of the RNA equivalent of at least one of the nucleotide sequences represented by any of SEQ ID NOs 99, 100, 527, 111, 112, 113, 114, 115, 116, 117, 536, 537, 538, 101, 102, 528, 97, 98, 526, 124, 106, 531, 109, 534, 126, 119, 127, 103, 104, 105, 529, 118, 108, 533, 121, 125, 123, 107, 532, 122, 120, 110, 535, 530, 539, 540, 541, 542, 543, 544, 545, 546, 547, 548, 549, 550, 551, 552 and 562 to 859, or comprising at least one double-stranded fragment of at least 17, preferably at least 18, 19, 20 or 21, more preferably at least 22, 23 or 24 basepairs in length thereof. Preferably, said double-stranded RNA comprises the RNA equivalent of the nucleotide sequence as represented in SEQ ID NO 117, or a double-stranded fragment of at least 17, preferably at least 18, 19, 20 or 21, more preferably at least 22, 23 or 24 basepairs in length thereof.
Accordingly, the present invention extends to methods as described herein, wherein the dsRNA 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 fungal target gene, and which comprises at least one additional dsRNA region, at least one strand of which comprises a nucleotide sequence which is complementary to at least part of the nucleotide sequence of at least one other fungal target gene. Such further target gene may be any of the target genes herein described. According to one preferred embodiment the dsRNA hits at least one target gene that is essential for viability, growth, development or reproduction of the fungus and hits at least one gene involved in pathogenicity or infectivity as described hereinabove. Alternatively, the dsRNA hits multiple genes of the same category, for example, the dsRNA hits at least 2 essential genes or at least 2 genes involved in pathogenicity or at least two genes involved in any of the cellular functions as described in Table 1.
Accordingly, the present invention extends to methods as described herein, wherein the dsRNA 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 fungal target gene, and which comprises the RNA equivalents of at least two nucleotide sequences independently chosen from each other. In one embodiment, the dsRNA comprises the RNA equivalents of at least two, preferably at least three, four or five, nucleotide sequences independently chosen from the sequences represented by any of SEQ ID Nos 99, 100, 527, 111, 112, 113, 114, 115, 116, 117, 536, 537, 538, 101, 102, 528, 97, 98, 526, 124, 106, 531, 109, 534, 126, 119, 127, 103, 104, 105, 529, 118, 108, 533, 121, 125, 123, 107, 532, 122, 120, 110, 535, 530, 539, 540, 541, 542, 543, 544, 545, 546, 547, 548, 549, 550, 551, 552 and 562 to 859, or fragments thereof of at least 17 basepairs in length, preferably at least 18, 19, 20 or 21, more preferably at least 22, 23 or 24 basepairs in length thereof.
The at least two nucleotide sequences may be derived from the target genes herein described. According to one preferred embodiment the dsRNA hits at least one target gene that is essential for viability, growth, development or reproduction of the nematode and hits at least one gene involved in pathogenicity or infectivity as described hereinabove. Alternatively, the dsRNA hits multiple genes of the same category, for example, the dsRNA hits at least 2 essential genes or at least 2 genes involved in the same cellular function.
According to a further embodiment, the dsRNA hits at least 2 target genes, which target genes are involved in a different cellular function chosen from those functions as described in Table 1. For example the dsRNA hits 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) such as the genes shown in FIGS. 3A-3MM.
The dsRNA regions (or fragments) in the double-stranded RNA may be combined as follows:
In addition, the target gene(s) to be combined may be chosen from one or more of the following categories of genes:
According to the invention, all double-stranded RNA regions comprise at least one strand that is complementary to at least part or a portion of the nucleotide sequence of any of the target genes herein described.
However, provided that one of the double-stranded RNA regions comprises at least one strand that is complementary to a portion of the nucleotide sequence of any one of the target genes herein described, the other double-stranded RNA regions may comprise at least one strand that is complementary to a portion of any other fungal target gene (including known target genes).
In one embodiment of the present invention, there is provided an isolated double-stranded RNA or RNA construct for use as a medicament.
According to yet another embodiment of the present invention, there is provided an isolated double-stranded RNA or RNA construct, further comprising at least one additional sequence and optionally a linker. In one embodiment, the additional sequence is chosen from the group comprising (i) a sequence facilitating large-scale production of the dsRNA construct; (ii) a sequence effecting an increase or decrease in the stability of the dsRNA; (iii) a sequence allowing the binding of proteins or other molecules to facilitate uptake of the RNA construct by a fungal cell(s); (iv) a sequence which is an aptamer that binds to a receptor or to a molecule on the surface or in the cytoplasm of a fungal cell(s) to facilitate uptake, endocytosis and/or transcytosis by the fungal cell(s); or (v) additional sequences to catalyze processing of dsRNA regions. In one embodiment, the linker is a conditionally self-cleaving RNA sequence, preferably a pH sensitive linker or a hydrophobic sensitive linker. In one embodiment, the linker is an intron.
In one embodiment, the multiple dsRNA regions of the double-stranded RNA construct are connected by one or more linkers. In another embodiment, the linker is present at a site in the RNA construct, separating the dsRNA regions from another region of interest. Different linker types for the dsRNA constructs are provided by the present invention.
In another embodiment, the multiple dsRNA regions of the double-stranded RNA construct are connected without linkers.
In a particular embodiment of the invention, 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 regions under particular circumstances, resulting in the release of separate dsRNA regions under these circumstances and leading to more efficient gene silencing by these smaller dsRNA regions. Examples of suitable conditionally self-cleaving linkers are RNA sequences that are self-cleaving at high 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 from the catalytic core of the hammerhead ribozyme HH16.
In another aspect of the invention, a linker is located at a site in the RNA construct, separating the dsRNA regions from another, e.g. the additional, sequence of interest, which preferably provides some additional function to the RNA construct.
In one particular embodiment of the invention, the dsRNA constructs of the present invention are provided with an aptamer to facilitate uptake of the dsRNA by the fungus. The aptamer is designed to bind a substance which is taken up by the fungus. Such substances may be from a fungal or plant origin. One specific example of an aptamer, is an aptamer that binds to a transmembrane protein, for example a transmembrane protein of a fungus. Alternatively, the aptamer may bind a (plant) metabolite or nutrient which is taken up by the fungus.
Alternatively, the linkers are self-cleaving in the endosomes. This may be advantageous when the constructs of the present invention are taken up by the fungus via endocytosis or transcytosis, and are therefore compartmentalized in the endosomes of the fungus species. The endosomes may have a low pH environment, leading to cleavage of the linker.
The above mentioned linkers that are self-cleaving in hydrophobic conditions are particularly useful in dsRNA constructs 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 fungus pest organism.
An intron may also 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 constructs 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) start at the 5′ end with -AG:GT- or —CG:GT- and/or (4) have at their 3′ end -AG:GC—or -AG:AA.
A non-complementary RNA sequence, ranging from about 1 base pair to about 10,000 base pairs, may also be used as a linker.
Without wishing to be bound by any particular theory or mechanism, it is thought that long double-stranded RNAs added externally to a fungal cell are taken up into the cell by the natural mechanisms by which fungal cells take up material from their immediate environment, such as for example pathways of endocytosis. Double-stranded RNAs taken up into the cell are then processed within the cell into short double-stranded RNAs, called small interfering RNAs (siRNAs), by the action of an endogenous endonuclease. The resulting siRNAs then mediate RNAi via formation of a multi-component RNase complex termed the RISC or RNA interfering silencing complex.
In order to achieve down-regulation of a target gene within a fungal cell the double-stranded RNA added to the exterior of the cell wall may be any dsRNA or dsRNA construct that can be taken up into the cell and then processed within the cell into siRNAs, which then mediate RNAi, or the RNA added to the exterior of the cell could itself be an siRNA that can be taken up into the cell and thereby direct RNAi.
siRNAs are generally short double-stranded RNAs having a length in the range of from 19 to 25 base pairs, or from 20 to 24 base pairs. In preferred embodiments siRNAs having 19, 20, 21, 22, 23, 24 or 25 base pairs, and in particular 21 or 22 base pairs, corresponding to the target gene to be down-regulated may be used. However, the invention is not intended to be limited to the use of such siRNAs.
siRNAs may include single-stranded overhangs at one or both ends, flanking the double-stranded portion. In a particularly preferred embodiment the siRNA may contain 3′ overhanging nucleotides, preferably two 3′ overhanging thymidines (dTdT) or uridines (UU). 3′ TT or UU overhangs may be included in the siRNA if the sequence of the target gene immediately upstream of the sequence included in double-stranded part of the dsRNA is AA. This allows the TT or UU overhang in the siRNA to hybridise to the target gene. Although a 3′ TT or UU overhang may also be included at the other end of the siRNA it is not essential for the target sequence downstream of the sequence included in double-stranded part of the siRNA to have AA. In this context, siRNAs which are RNA/DNA chimeras are also contemplated. These chimeras include, for example, the siRNAs comprising a double-stranded RNA with 3′ overhangs of DNA bases (e.g. dTdT), as discussed above, and also double-stranded RNAs which are polynucleotides in which one or more of the RNA bases or ribonucleotides, or even all of the ribonucleotides on an entire strand, are replaced with DNA bases or deoxynucleotides.
The dsRNA may be formed from two separate (sense and antisense) RNA strands that are annealed together by (non-covalent) basepairing. Alternatively, 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 stands of the dsRNA are formed from different regions of single polynucleotide molecule that is partially self-complementary. RNAs having this structure are convenient if the dsRNA is to be synthesised by expression in vivo, for example in a host cell or organism as discussed below, or by in vitro transcription. The precise nature and sequence of the “loop” linking the two RNA strands is generally not material to the invention, except that it should not impair the ability of the double-stranded part of the molecule to mediate RNAi. The features of “hairpin” or “stem-loop” RNAs for use in RNAi are generally known in the art (see for example WO 99/53050, in the name of CSIRO, the contents of which are incorporated herein by reference). In other embodiments of the invention, the loop structure may comprise linker sequences or additional sequences as described above.
The double-stranded RNA or construct may be prepared in a manner known per se. For example, double-stranded RNAs may be synthesised in vitro using chemical or enzymatic RNA synthesis techniques well known in the art. In one approach the two separate RNA strands may be synthesised separately and then annealed to form double-strands. In a further embodiment, double-stranded RNAs or constructs may be synthesised by intracellular expression in a host cell or organism from a suitable expression vector. This approach is discussed in further detail below.
The amount of double-stranded RNA with which the fungal cell is contacted is such that specific down-regulation of the one or more target genes is achieved. The RNA may be introduced in an amount which allows delivery of at least one copy per cell. However, in certain embodiments higher doses (e.g., at least 5, 10, 100, 500 or 1000 copies per cell) of double-stranded RNA may yield more effective inhibition. For any given fungal gene target the optimum amount of dsRNA for effective inhibition may be determined by routine experimentation.
The fungal cell may be contacted with the double-stranded RNA in any suitable manner, permitting direct uptake of the double-stranded RNA by the fungus. For example, the fungal cell can be contacted with the double-stranded RNA in pure or substantially pure form, for example an aqueous solution containing the dsRNA. In this embodiment, the fungus may be simply “soaked” with an aqueous solution comprising the double-stranded RNA. In a further embodiment the fungal cell can be contacted with the double-stranded RNA by spraying the fungal cell with a liquid composition comprising the double-stranded RNA.
Alternatively, the double-stranded RNA may be linked to a food component of the fungi, such as a food component for a mammalian pathogenic fungus, in order to increase uptake of the dsRNA by the fungus.
In other embodiments the fungal cell may be contacted with a composition containing the double-stranded RNA. The composition may, in addition to the dsRNA, contain further excipients, diluents or carriers. Preferred features of such compositions are discussed in more detail below.
The double-stranded RNA may also be incorporated in the medium in which the fungus grows or in or on a material or substrate that is infested by the fungus or impregnated in a substrate or material susceptible to infestation by fungus.
Another aspect of the present invention are target nucleotide sequences of the fungal target genes herein disclosed. Such target nucleotide sequences are particularly important to design the dsRNA constructs according to the present invention. Such target nucleotide sequences are preferably at least 17, preferably at least 18, 19, 20 or 21, more preferably at least 22, 23 or 24 nucleotides in length. Non-limiting examples of preferred target nucleotide sequences are given in the examples. The present invention encompasses isolated nucleotide sequences consisting of at least one sequence represented by any of SEQ ID NOs 3, 42, 99, 100, 527, 39, 60, 111, 112, 113, 114, 115, 116, 117, 536, 537, 538, 5, 43, 101, 102, 528, 1, 41, 97, 98, 526, 184, 185, 37, 59, 124, 9, 45, 106, 531, 188, 189, 13, 47, 109, 534, 33, 57, 126, 23, 52, 119, 35, 58, 127, 7, 44, 103, 104, 105, 529, 186, 187, 29, 55, 118, 17, 49, 108, 533, 25, 53, 121, 19, 50, 125, 31, 56, 123, 11, 46, 107, 532, 27, 54, 122, 21, 51, 120, 15, 48, 110, 535, 458, 486, 530, 460, 487, 539, 540, 462, 488, 541, 464, 489, 542, 466, 490, 543, 468, 491, 544, 470, 492, 545, 472, 493, 546, 474, 494, 547, 476, 496, 548, 478, 556, 549, 480, 497, 550, 482, 498, 551, 484, 499 and 552 and 562 to 859 or the complement thereof, comprising a fragment thereof comprising at least 17, preferably at least 18, 19, 20 or 21, more preferably at least 22, 23 or 24 nucleotides of any of SEQ ID 3, 42, 99, 100, 527, 39, 60, 111, 112, 113, 114, 115, 116, 117, 536, 537, 538, 5, 43, 101, 102, 528, 1, 41, 97, 98, 526, 184, 185, 37, 59, 124, 9, 45, 106, 531, 188, 189, 13, 47, 109, 534, 33, 57, 126, 23, 52, 119, 35, 58, 127, 7, 44, 103, 104, 105, 529, 186, 187, 29, 55, 118, 17, 49, 108, 533, 25, 53, 121, 19, 50, 125, 31, 56, 123, 11, 46, 107, 532, 27, 54, 122, 21, 51, 120, 15, 48, 110, 535, 458, 486, 530, 460, 487, 539, 540, 462, 488, 541, 464, 489, 542, 466, 490, 543, 468, 491, 544, 470, 492, 545, 472, 493, 546, 474, 494, 547, 476, 496, 548, 478, 556, 549, 480, 497, 550, 482, 498, 551, 484, 499 and 552 and 562 to 859 or the complement thereof.
According to one embodiment, the present invention provides an isolated nucleotide sequence encoding a double-stranded RNA or double-stranded RNA construct as described herein.
According to yet another embodiment, the present invention provides fungal target genes, which comprise a sequence as herein represented by SEQ ID NO 192, 117, 201, 202, 193, 190, 191, 196, 199, 200, 194, 195, 198 and 197, or a fragment thereof of at least 17, preferably at least 18, 19, 20 or 21, more preferably at least 22, 23 or 24 nucleotides thereof, and which target genes are encompassed by the methods of the present invention.
According to a more specific embodiment, the present invention relates to an isolated nucleic acid sequence consisting of a sequence represented by any of SEQ ID NOs 3, 99, 100, 527, 192, 39, 111, 112, 113, 114, 115, 116, 117, 536, 537, 538, 201, 202, 5, 101, 102, 528, 193, 1, 97, 98, 526, 184, 185, 190, 191, 37, 124, 9, 106, 531, 188, 189, 196, 13, 109, 534, 199, 200, 33, 126, 23, 119, 35, 127, 7, 103, 104, 105, 529, 186, 187, 194, 195, 29, 118, 17, 108, 533, 198, 25, 121, 19, 125, 31, 123, 11, 107, 532, 197, 27, 122, 21, 120, 15, 110, 535, 458, 530, 460, 539, 540, 462, 541, 464, 542, 466, 543, 468, 544, 470, 545, 472, 546, 474, 547, 476, 548, 478, 549, 480, 550, 482, 551, 484, 552 and 562 to 859, or a fragment of at least 17 preferably at least 18, 19, 20 or 21, more preferably at least 22, 23 or 24 nucleotides thereof.
A person skilled in the art will recognize that homologues of these target genes can be found and that these homologues are also useful in the methods of the present invention.
Protein, or nucleotide sequences are likely to be homologous if they show a “significant” level of sequence similarity. Truely homologous sequences are related by divergence from a common ancestor gene. Sequence homologues can be of two types: (i) where homologues exist in different species they are known as orthologues. e.g. the α-globin genes in mouse and human are orthologues. (ii) paralogues are homologous genes in within a single species. e.g. the α- and β-globin genes in mouse are paralogues.
Preferred homologues are genes comprising a sequence which is at least about 85% or 87.5%, still more preferably about 90%, still more preferably at least about 95% and most preferably at least about 99% identical to a sequence selected from the group of sequences represented by SEQ ID NOs 3, 42, 99, 100, 527, 39, 60, 111, 112, 113, 114, 115, 116, 117, 536, 537, 538, 5, 43, 101, 102, 528, 1, 41, 97, 98, 526, 184, 185, 37, 59, 124, 9, 45, 106, 531, 188, 189, 13, 47, 109, 534, 33, 57, 126, 23, 52, 119, 35, 58, 127, 7, 44, 103, 104, 105, 529, 186, 187, 29, 55, 118, 17, 49, 108, 533, 25, 53, 121, 19, 50, 125, 31, 56, 123, 11, 46, 107, 532, 27, 54, 122, 21, 51, 120, 15, 48, 110, 535, 458, 486, 530, 460, 487, 539, 540, 462, 488, 541, 464, 489, 542, 466, 490, 543, 468, 491, 544, 470, 492, 545, 472, 493, 546, 474, 494, 547, 476, 496, 548, 478, 556, 549, 480, 497, 550, 482, 498, 551, 484, 499, 552 and 562 to 859, or the complement thereof. Methods for determining sequence identity are routine in the art and include use of the Blast software and EMBOSS software (The European Molecular Biology Open Software Suite (2000), Rice, P. Longden, I. and Bleasby, A. Trends in Genetics 16, (6) pp 276-277). The term “identity” as used herein refers to the relationship between sequences at the nucleotide level. The expression “% identical” is determined by comparing optimally aligned sequences, e.g. two or more, over a comparison window wherein the portion of the sequence in the comparison window may comprise insertions or deletions as compared to the reference sequence for optimal alignment of the sequences. The reference sequence does not comprise insertions or deletions. The reference window is chosen from between at least 10 contiguous nucleotides to about 50, about 100 or to about 150 nucleotides, preferably between about 50 and 150 nucleotides. “% identity” is then calculated by determining the number of nucleotides that are identical between the sequences in the window, dividing the number of identical nucleotides by the number of nucleotides in the window and multiplying by 100.
Other homologues are genes which are alleles of a gene comprising a sequence as represented by any of SEQ ID NOs 3, 42, 99, 100, 527, 39, 60, 111, 112, 113, 114, 115, 116, 117, 536, 537, 538, 5, 43, 101, 102, 528, 1, 41, 97, 98, 526, 184, 185, 37, 59, 124, 9, 45, 106, 531, 188, 189, 13, 47, 109, 534, 33, 57, 126, 23, 52, 119, 35, 58, 127, 7, 44, 103, 104, 105, 529, 186, 187, 29, 55, 118, 17, 49, 108, 533, 25, 53, 121, 19, 50, 125, 31, 56, 123, 11, 46, 107, 532, 27, 54, 122, 21, 51, 120, 15, 48, 110, 535, 458, 486, 530, 460, 487, 539, 540, 462, 488, 541, 464, 489, 542, 466, 490, 543, 468, 491, 544, 470, 492, 545, 472, 493, 546, 474, 494, 547, 476, 496, 548, 478, 556, 549, 480, 497, 550, 482, 498, 551, 484, 499, 552 and 562 to 859. Further preferred homologues are genes comprising at least one single nucleotide polymorphism (SNP) compared to a gene comprising a sequence as represented by any of SEQ ID NOs 3, 42, 99, 100, 527, 39, 60, 111, 112, 113, 114, 115, 116, 117, 536, 537, 538, 5, 43, 101, 102, 528, 1, 41, 97, 98, 526, 184, 185, 37, 59, 124, 9, 45, 106, 531, 188, 189, 13, 47, 109, 534, 33, 57, 126, 23, 52, 119, 35, 58, 127, 7, 44, 103, 104, 105, 529, 186, 187, 29, 55, 118, 17, 49, 108, 533, 25, 53, 121, 19, 50, 125, 31, 56, 123, 11, 46, 107, 532, 27, 54, 122, 21, 51, 120, 15, 48, 110, 535, 458, 486, 530, 460, 487, 539, 540, 462, 488, 541, 464, 489, 542, 466, 490, 543, 468, 491, 544, 470, 492, 545, 472, 493, 546, 474, 494, 547, 476, 496, 548, 478, 556, 549, 480, 497, 550, 482, 498, 551, 484, 499, 552 and 562 to 859.
According to another embodiment, the invention encompasses target genes which are fungal orthologues of a gene comprising any of SEQ ID Nos 206 to 458. Preferred orthologues are represented by any of SEQ ID NOs 206 to 353. More preferred orthologues are represented by any of SEQ ID NOs 206 to 337.
In one embodiment, the present invention relates to any method described herein wherein a nucleic acid is used encoding a protein with an amino acid sequence which is at least 75%, at least 80% or 85% identical, preferably at least 90%, 95%, 96%, or more preferably at least 97%, 98% and still more preferably at least 99% identical to the amino acid sequence as given in SEQ ID NOs 2, 4, 6, 8, 10, 12, 18, 14, 16, 40, 30, 24, 22, 26, 28, 32, 38, 20, 34, 36, 459, 461, 463, 465, 467, 469, 471, 473, 475, 477, 479, 481, 483 and 485.
In another embodiment, the present invention relates to any method described herein wherein a nucleic acid is used encoding a protein with an amino acid sequence which is at least 75%, at least 80% or 85% similar, preferably at least 90%, 95%, 96%, or more preferably at least 97%, 98% and still more preferably at least 99% similar to the amino acid sequence as given in SEQ ID NOs 2, 4, 6, 8, 10, 12, 18, 14, 16, 40, 30, 24, 22, 26, 28, 32, 38, 20, 34, 36, 459, 461, 463, 465, 467, 469, 471, 473, 475, 477, 479, 481, 483 and 485.
The term “similar” or “similarity” with respect to amino acid sequences allows, for instance, conservative amino acid substitutions to be introduced at one or more positions in the amino acid sequences of target polypeptides. A “conservative amino acid substitution” is one in which the amino acid is replaced by another amino acid having a similar structure and/or chemical function. Families of amino acid residues having similar structures and functions are well known. These families include amino acids with basic side chains (e.g. lysine, arginine, histidine), acidic side chains (e.g. aspartic acid, glutamic acid), uncharged polar side chains (e.g., glycine, asparagine, glutamine, serine, threonine, tyrosine, cysteine), nonpolar side chains (e.g. alanine, valine, leucine, isoleucine, praline, phenylalanine, methionine, tryptophan), beta- branched side chains (e.g. threonine, valine, isoleucine) and aromatic side chains (e.g. tyrosine, phenylalanine, tryptophan, histidine). BLAST, BLAST 2.0 and BLAST 2.2.2 algorithms are also used to define “identity” and “similarity” according to the invention. They are described, e.g., in Altschul (1977) Nuc. Acids Res. 25:3389 3402; Altschul (1990) J. Mol. Biol. 215:403-410. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information.
In one embodiment, the present invention relates to a nucleic acid which is degenerated to a nucleic acid encoding a protein as given in any of SEQ ID NOs 2, 4, 6, 8, 10, 12, 18, 14, 16, 40, 30, 24, 22, 26, 28, 32, 38, 20, 34, 36, 459, 461, 463, 465, 467, 469, 471, 473, 475, 477, 479, 481, 483 and 485, as a result of the genetic code.
In another embodiment, the present invention relates to a nucleic acid which is diverging from a nucleic acid encoding a protein as given in any of SEQ ID NOs 2, 4, 6, 8, 10, 12, 18, 14, 16, 40, 30, 24, 22, 26, 28, 32, 38, 20, 34, 36, 459, 461, 463, 465, 467, 469, 471, 473, 475, 477, 479, 481, 483 and 485, as a result of differences in codon usage between organisms.
In yet another embodiment, the present invention relates to a nucleic acid which is diverging from a nucleic acid encoding a protein as given in any of SEQ ID NOs 2, 4, 6, 8, 10, 12, 18, 14, 16, 40, 30, 24, 22, 26, 28, 32, 38, 20, 34, 36, 459, 461, 463, 465, 467, 469, 471, 473, 475, 477, 479, 481, 483 and 485, as a result of differences between alleles.
The invention also encompasses target genes which are fungal orthologues of a gene encoding any of the polypeptides of SEQ ID Nos 2, 4, 6, 8, 10, 12, 18, 14, 16, 40, 30, 24, 22, 26, 28, 32, 38, 20, 34, 36, 459, 461, 463, 465, 467, 469, 471, 473, 475, 477, 479, 481, 483 and 485.
According to another embodiment, the invention encompasses target genes which are fungal orthologues of a gene comprising a nucleotide sequence as represented in any of SEQ ID Nos 562 to 746. A non-limiting list of fungal orthologues genes or sequences comprising at least a fragment of 17 nucleotides of one of the sequences of the invention is given in Table 8. By way of example, orthologues may comprise a nucleotide sequence as represented in any of SEQ ID NOs 562 to 746, or a fragment of at least 17, 18, 19, 20, 21, 22, 23, 24, 25, 26 or 27 nucleotides thereof. According to another aspect, the invention thus encompasses any of the methods described herein for controlling fungal growth on a cell or an organism, or for preventing fungal infestation of a cell or an organism susceptible to fungal infection, comprising contacting nematodes with a double-stranded RNA, wherein the double-stranded RNA comprises annealed complementary strands, one of which has a nucleotide sequence which is complementary to at least part of the nucleotide sequence of a target gene comprising a fragment of at least 17, 18, 19, 20 or 21 nucleotides of any of the sequences as represented in SEQ ID NOs 562 to 746, whereby the double-stranded RNA is taken up by the fungus and thereby controls growth or prevents infestation. The invention also relates to fungal-resistant transgenic plants comprising a fragment of at least 17, 18, 19, 20 or 21 nucleotides of any of the sequences as represented in SEQ ID NOs 562 to 746. Said fungus may be one of the following non-limiting list of Table 8.
According to another embodiment, the invention encompasses target genes which are nematode orthologues of a gene comprising a nucleotide sequence as represented in any of SEQ ID Nos 747 to 790. A non-limiting list of nematode orthologues genes or sequences comprising at least a fragment of 17 nucleotides of one of the sequences of the invention is given in Table 9. By way of example, orthologues may comprise a nucleotide sequence as represented in any of SEQ ID NOs 747 to 790, or a fragment of at least 17, 18, 19, 20, 21, 22, 23, 24, 25, 26 or 27 nucleotides thereof. According to another aspect, the invention thus encompasses any of the methods described herein for controlling nematode growth in an organism, or for preventing nematode infestation of an organism susceptible to nematode infection, comprising contacting nematodes with double-stranded RNA, wherein the double-stranded RNA comprises annealed complementary strands, one of which has a nucleotide sequence which is complementary to at least part of the nucleotide sequence of a target gene comprising a fragment of at least 17, 18, 19, 20 or 21 nucleotides of any of the sequences as represented in SEQ ID NOs 747 to 790, whereby the double-stranded RNA is taken up by the nematode and thereby controls growth or prevents infestation. The invention also relates to nematode-resistant transgenic plants comprising a fragment of at least 17, 18, 19, 20 or 21 nucleotides of any of the sequences as represented in SEQ ID NOs 747 to 790. Said nematode may be one of the following non-limiting list of Table 9.
According to another embodiment, the invention encompasses target genes which are insect orthologues of a gene comprising a nucleotide sequence as represented in any of SEQ ID Nos 791 to 859. A non-limiting list of fungal orthologues genes or sequences comprising at least a fragment of 17 nucleotides of one of the sequences of the invention is given in Table 10. By way of example, orthologues may comprise a nucleotide sequence as represented in any of SEQ ID NOs 791 to 859, or a fragment of at least 17, 18, 19, 20, 21, 22, 23, 24, 25, 26 or 27 nucleotides thereof. According to another aspect, the invention thus encompasses any of the methods described herein for controlling insect growth on a cell or an organism, or for preventing insect infestation of a cell or an organism susceptible to insect infection, comprising contacting insects with a double-stranded RNA, wherein the double-stranded RNA comprises annealed complementary strands, one of which has a nucleotide sequence which is complementary to at least part of the nucleotide sequence of a target gene comprising a fragment of at least 17, 18, 19, 20 or 21 nucleotides of any of the sequences as represented in SEQ ID NOs 791 to 859, whereby the double-stranded RNA is taken up by the insect and thereby controls growth or prevents infestation. The invention also relates to insect-resistant transgenic plants comprising a fragment of at least 17, 18, 19, 20 or 21 nucleotides of any of the sequences as represented in SEQ ID NOs 791 to 859. Said insect may be one of the following non-limiting list of Table 10.
In one preferred embodiment of the invention the dsRNA may be expressed by (e.g. transcribed within) a host cell or host organism, the host cell or organism being an organism susceptible or vulnerable to infestation with a fungus. In this embodiment RNAi-mediated gene silencing of one or more target genes in the fungus may be used as a mechanism to control growth of the fungus in or on the host organism and/or to prevent or reduce fungal infestation of the host organism. Thus, expression of the double-stranded RNA within cells of the host organism may confer resistance to a particular fungus or to a class of fungi. In case the dsRNA hits more than one fungal target gene, expression of the double-stranded RNA within cells of the host organism may confer resistance to more than one fungus or more than one class of fungi.
In a preferred embodiment the host organism is a plant and the fungus is a plant pathogenic fungus. In this embodiment the fungal cell is contacted with the double-stranded RNA by expressing the double-stranded RNA in a plant or plant cell that is infested with or susceptible to infestation with the plant pathogenic fungus.
In this context the term “plant” encompasses any plant material that it is desired to treat to prevent or reduce fungal growth and/or fungal infestation. This includes, inter alia, whole plants, seedlings, propagation or reproductive material such as seeds, cuttings, grafts, explants, etc. and also plant cell and tissue cultures. The plant material should express, or have the capability to express, dsRNA corresponding to one or more target genes of the fungus.
Therefore, in a further aspect the invention provides a plant, preferably a transgenic plant, or propagation or reproductive material for a (transgenic) plant, or a plant cell culture expressing or capable of expressing at least one double-stranded RNA, wherein the 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 of a fungus, such that the double-stranded RNA is taken up by a fungal cell upon plant-fungus interaction, said double-stranded RNA being capable of inhibiting the target gene or down-regulating expression of the target gene by RNA interference. The target gene may be any of the target genes herein described, for instance a target gene that is essential for the viability, growth, development or reproduction of the fungus, preferably said fungal target gene is involved in any of the cellular functions as defined in Table 1; or for instance a fungal target gene that is involved in the pathogenicity or infectivity of the fungus, preferably said fungal target gene is involved in the formation of germ tubes, conidia attachment, formation of appressoria, formation of the penetration peg or formation of conidia.
In this embodiment the fungal cell can be any fungal cell, but is preferably a fungal cell of a plant pathogenic fungus. Preferred plant pathogenic fungi include, but are not limited to, those listed above.
A plant to be used in the methods of the invention, or a transgenic plant according to the invention encompasses any plant, but is preferably a plant that is susceptible to infestation by a plant pathogenic fungus, including but not limited to the following plants: rice, corn, soybean, cotton, potato, banana or tomato, cereals including wheat, oats, barley, rye, vine, apple, pear, sorghum, millet, beans, groundnuts, rapeseed, sunflower, sugarcane. Most preferably the plant is rice, corn, soybean, cotton, potato, banana or tomato.
Accordingly, the present invention extends to methods as described herein wherein the plant is wheat, sorghum, millet, beans, groundnuts, rapeseed, sunflower, sugarcane, rice, corn, soybean, cotton, potato, banana or tomato. In a preferred embodiment the plant is rice, corn, soybean, cotton, potato, banana or tomato.
In one embodiment the present invention extends to methods as described herein, wherein the plant is rice and the target gene is a gene from a fungus selected from the group consisting of: Magnaporthe spp. (e.g. Magnaporthe oryzae or Magnaporthe grisae), Rhizoctonia spp. (e.g. Rhizoctonia solani, Rhizoctonia oryzae or Rhizoctonia cerealis), Fusarium spp. (e.g. Fusarium roseum), Acremoniella spp. (e.g. Acremoniella atra), Pythium spp. (e.g. Pythium arrhenomanes, P. myriotylum, or P. dissotocum), Curvularia spp. (e.g. Curvularia oryzae, Curvularia lunatas), Trichoderma spp. (e.g. Trichoderma virde) and Rhizopus spp. (e.g. Rhizopus chinensis); in another embodiment the present invention extends to methods as described herein, wherein the plant is corn and the target gene is a gene from a fungus selected from the group consisting of: Colletotrichum spp. (e.g. Colletotrichum lindemuthianum), Gibberella spp., Fusarium spp. (e.g. Fusarium nivale, Fusarium oxysporum, Fusarium graminearum, Fusarium germinearum, Fusarium culmorum, Fusarium solani, Fusarium moniliforme or Fusarium roseum), Diplodia spp. (e.g. Diplodia maydis) or Puccina spp. (e.g. Puccinia sorgh, Puccinia striiformis (causing yellow rust), Puccinia graminis f.sp. tritici, Puccinia asparag, Puccinia recondita or Puccinia arachidis); in another embodiment the present invention extends to methods as described herein, wherein the plant is soybean and the target gene is a gene selected from fungus Phakopsora spp. (e.g. Phakopsora pachyrhizi); in another embodiment the present invention extends to methods as described herein, wherein the plant is cotton and the target gene is a gene from a fungus selected from the group consisting of Fusarium spp. (e.g. Fusarium nivale, Fusarium oxysporum, Fusarium graminearum, Fusarium germinearum, Fusarium culmorum, Fusarium solani, Fusarium moniliforme or Fusarium roseum) or Verticillium spp. (e.g. Verticillium dahliae or Verticillium albo-atrum); in another embodiment the present invention extends to methods as described herein, wherein the plant is potato and the target gene is a gene from a fungus selected from the group consisting of Phytophthora spp. (e.g. Phytophthora cinnamomi, Phytophthora cactorum, Phytophthora phaseoli, Phytophthora parasitica, Phytophthora citrophthora, Phytophthora megasperma f.sp. soiae or Phytophthora infestans), Rhizoctonia spp. (e.g. Rhizoctonia solani, Rhizoctonia oryzae or Rhizoctonia cerealis) or a fungal species that causes wilt, rot or scurf; in another embodiment the present invention extends to methods as described herein, wherein the plant is banana and the target gene is a gene from a fungus selected from the group consisting of Mycosphaerella spp., Cercospora spp. (e.g. Cercospora kikuchii or Cercospora zaea-maydis) or Fusarium spp. (e.g. Fusarium nivale, Fusarium oxysporum, Fusarium graminearum, Fusarium germinearum, Fusarium culmorum, Fusarium solani, Fusarium moniliforme or Fusarium roseum); in another embodiment the present invention extends to methods as described herein, wherein the plant is tomato and the target gene is a gene from a fungus selected from the group consisting of Phytophthora spp. (e.g. Phytophthora cinnamom, Phytophthora cactorum, Phytophthora phaseoli, Phytophthora parasitica, Phytophthora citrophthora, Phytophthora megasperma f.sp. soiae or Phytophthora infestans) or a fungal species that causes foliar disease, wilt or fruit rot.
In a specific embodiment the plant is rice and the fungus is Magnaporthe oryzae causing e.g. rice blast. In another specific embodiment the plant is rice and the fungus is Rhizoctonia spp. (e.g. Rhizoctonia solani, Rhizoctonia oryzae or Rhizoctonia cerealis) causing e.g. sheath blight. In yet another embodiment the plant is rice and the fungus is Rhizoctonia spp. (e.g. Rhizoctonia solani, Rhizoctonia oryzae or Rhizoctonia cerealis), Fusarium spp. (e.g. Fusarium roseum), Acremoniella spp. (e.g. Acremoniella atra), Pythium spp. (e.g. Pythium arrhenomanes, P. myriotylum, or P. dissotocum), Curvularia spp. (e.g. Curvularia oryzae, Curvularia lunatas), Trichoderma spp. (e.g. Trichoderma virde) or Rhizopus spp. (e.g. Rhizopus chinensis) causing seedling blight; in another specific embodiment the plant is soybean and the fungus is Phakopsora spp. (e.g. Phaopsora pachyrhizi) causing e.g. soybean rust; in another specific embodiment the plant is potato and the fungus is Phytophthora spp. (e.g. Phytophthora cinnamomi, Phytophthora cactorum, Phytophthora phaseoli, Phytophthora parasitica, Phytophthora citrophthora, Phytophthora megasperma f.sp. soiae or Phytophthora infestans) causing e.g. late blight; in another specific embodiment the plant is banana and the fungus is Cercospora spp. (e.g. Cercospora kikuchii or Cercospora zaea-maydis) or Mycosphaerella spp. causing e.g. black and yellow sigatoka. In another specific embodiment the plant is banana and the fungus is Fusarium spp. (e.g. Fusarium nivale, Fusarium oxysporum, Fusarium graminearum, Fusarium germinearum, Fusarium culmorum, Fusarium solani, Fusarium moniliforme or Fusarium roseum) causing e.g. Panama disease; in another specific embodiment the plant is tomato and the fungus is Phytophthora spp. (e.g. Phytophthora cinnamomi, Phytophthora cactorum, Phytophthora phaseoli, Phytophthora parasitica, Phytophthora citrophthora, Phytophthora megasperma f.sp. soiae or Phytophthora infestans) causing e.g. late blight; in yet another specific embodiment the plant is corn and the fungus is Colletotrichum spp. (e.g. Colletotrichum lindemuthianum) causing e.g. anthracnose. In another specific embodiment the plant is corn and the fungus is Diplodia spp. (e.g. Diplodia maydis), Fusarium spp. (e.g. Fusarium nivale, Fusarium oxysporum, Fusarium graminearum, Fusarium germinearum, Fusarium culmorum, Fusarium solani, Fusarium moniliforme or Fusarium roseum) or Gibberella spp. causing e.g. ear, kernel and stalk rots. In another specific embodiment the plant is corn and the fungus is Puccinia spp. (e.g. Puccinia sorghi, Puccinia striiformis, Puccinia graminis f.sp. tritici, Puccinia asparagi, Puccinia recondita or Puccinia arachidis) causing e.g. common rust; in another specific embodiment the plant is cotton and the fungus is Fusarium spp. (e.g. Fusarium nivale, Fusarium oxysporum, Fusarium graminearum, Fusarium germinearum, Fusarium culmorum, Fusarium solani, Fusarium moniliforme or Fusarium roseum) causing e.g. fusarium wilt. In another specific embodiment the plant is cotton and the fungus is Verticillium spp. (e.g. Verticillium dahliae or Verticillium albo-atrum) causing e.g. verticillium wilt; in another specific embodiment the plant is potato and the fungus is Rhizoctonia spp. (e.g. Rhizoctonia solani, Rhizoctonia oryzae or Rhizoctonia cerealis) causing e.g. early blight. In another specific embodiment the plant is potato and the fungus is a fungal species causing e.g. wilts, rots or scurf; in another specific embodiment the plant is tomato and the fungus is a fungal species causing e.g. foliar disease, wilts or fruit rots.
In another embodiment the present invention extends to methods as described herein, wherein the plant is rice and wherein said target gene is a gene coding for a fungal orthologue of a protein selected from the group of proteins whose function is given in Table 1.
Transgenic plants according to the invention extend to all plant species specifically described above being resistant to the respective fungus species as specifically described above. Preferred transgenic plants (or reproductive or propagation material for a transgenic plant, or a cultured transgenic plant cell) are plants (or reproductive or propagation material for a transgenic plant, or a cultured transgenic plant cell) wherein said fungal target gene comprises a sequence which is selected from the group comprising:
Transgenic plants according to the invention extend to all plant species specifically described above being resistant to the respective fungal species as specifically described above.
In one embodiment the transgenic plant (or reproductive or propagation material for a transgenic plant or a cultured transgenic plant cell) is a rice plant or reproductive or propagation material for a rice plant or a cultured rice plant cell, wherein the target gene is a gene from a fungus selected from the group comprising Magnaporthe spp., Rhizoctonia spp., Fusarium spp., Acremoniella spp., Pythium spp., Curvularia spp., Trichoderma spp. and Rhizopus spp.
In yet another embodiment the transgenic plant (or reproductive or propagation material for a transgenic plant or a cultured transgenic plant cell) is a rice, cotton, potato, tomato, corn, tobacco, banana or soybean plant or reproductive or propagation material of such a plant and wherein the target gene is coding for a fungal orthologue of a protein selected from the group of proteins whose function is given in Table 1.
The present invention also encompasses transgenic plants (or reproductive or propagation material for a transgenic plant, or a cultured transgenic plant cell) which express or are capable of expressing at least one of the nucleotides of the invention, for instance at least one of the nucleotide sequences represented in any of SEQ ID Nos 3, 42, 99, 100, 527, 39, 60, 111, 112, 113, 114, 115, 116, 117, 536, 537, 538, 5, 43, 101, 102, 528, 1, 41, 97, 98, 526, 184, 185, 37, 59, 124, 9, 45, 106, 531, 188, 189, 13, 47, 109, 534, 33, 57, 126, 23, 52, 119, 35, 58, 127, 7, 44, 103, 104, 105, 529, 186, 187, 29, 55, 118, 17, 49, 108, 533, 25, 53, 121, 19, 50, 125, 31, 56, 123, 11, 46, 107, 532, 27, 54, 122, 21, 51, 120, 15, 48, 110, 535, 458, 486, 530, 460, 487, 539, 540, 462, 488, 541, 464, 489, 542, 466, 490, 543, 468, 491, 544, 470, 492, 545, 472, 493, 546, 474, 494, 547, 476, 496, 548, 478, 556, 549, 480, 497, 550, 482, 498, 551, 484, 499, 552 and 562 to 859 or the complement thereof, or comprising a fragment thereof comprising at least 17, preferably at least 18, 19, 20 or 21, more preferably at least 22, 23 or 24 nucleotides.
The plant may be provided in a form wherein it is actively expressing (transcribing) the double-stranded RNA in one or more cells, cell types or tissues. Alternatively, the plant may be “capable of expressing”, meaning that it is transformed with a transgene which encodes the desired dsRNA but that the transgene is not active in the plant when (and in the form in which) the plant is supplied.
Therefore, according to another embodiment, a recombinant DNA construct is provided comprising the nucleotide sequence encoding the dsRNA or dsRNA construct according to the present invention operably linked to at least one regulatory sequence. Preferably, the regulatory sequence is selected from the group comprising constitutive promoters or tissue specific promoters as described in the invention.
The target gene may be any target gene herein described. Preferably the regulatory element is a regulatory element that is active in a plant cell. More preferably, the regulatory element is originating from a plant. The term “regulatory sequence” is to be taken in a broad context and refer to a regulatory nucleic acid capable of effecting expression of the sequences to which it is operably linked.
Encompassed by the aforementioned term are promoters and nucleic acids or synthetic fusion molecules or derivatives thereof which activate or enhance expression of a nucleic acid, so called activators or enhancers. The term “operably linked” as used herein refers to a functional linkage between the promoter sequence and the gene of interest, such that the promoter sequence is able to initiate transcription of the gene of interest.
By way of example, the transgene nucleotide sequence encoding the double-stranded RNA could be placed under the control of an inducible or growth or developmental stage-specific promoter which permits transcription of the dsRNA to be turned on, by the addition of the inducer for an inducible promoter or when the particular stage of growth or development is reached.
Alternatively, the transgene encoding the double-stranded RNA is placed under the control of a strong constitutive promoter such as any selected from the group comprising the CaMV35S promoter, doubled CaMV35S promoter, ubiquitin promoter, actin promoter, rubisco promoter, GOS2 promoter, Figwort mosaic viruse (FMV) 34S promoter.
Alternatively, the transgene encoding the double-stranded RNA is placed under the control of a tissue specific promoter 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 promoter of RJ39 from strawberry.
Furthermore, when using the methods of the present invention for developing transgenic plants resistant against fungi, it might be beneficial to place the nucleic acid encoding the double-stranded RNA according to the present invention under the control of a tissue-specific promoter. In order to improve the transfer of the dsRNA from the plant cell to the pest, the plants could preferably express the dsRNA in a plant part that is first accessed or damaged by the plant pest. In case of a plant pathogenic fungi, preferred tissues to express the dsRNA are the roots, leaves and stem. Therefore, in the methods of the present invention, a plant tissue-preferred promoter may be used, such as a root specific promoter, a leaf specific promoter or a stem-specific promoter. Suitable examples of a root specific promoter are PsMTA (Fordam-Skelton, A. P., et al., 1997 Plant Molecular Biology 34: 659-668.) and the Class III Chitinase promoter. 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).
In yet other embodiments of the present invention, other promoters useful for the expression of dsRNA are used and include, but are not limited to, promoters from an RNA Poll, an RNA PolII, an RNA PolIII, 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 antifungal agent, for example in an anti-fungal liquid, spray or powder.
Therefore, the present invention also encompasses a method for generating any of the double-stranded RNA or RNA constructs of the invention. This method comprises the steps of (a) contacting an isolated nucleic acid or a recombinant DNA construct of the invention with cell-free components; or (b) introducing (e.g. by transformation, transfection or injection) an isolated nucleic acid or a recombinant DNA construct of the invention in a cell, under conditions that allow transcription of said nucleic acid or recombinant DNA construct to produce the dsRNA or RNA construct.
In one embodiment of the present invention, there is provided a recombinant DNA construct as described herein for use as a medicament.
Accordingly, the present invention also encompasses a cell comprising any of the nucleotide sequences or recombinant DNA constructs described 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.
Optionally, one or more transcription termination sequences may also be incorporated in the recombinant construct of the invention. 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 recombinant 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) in a cell. Preferred origins of replication include, but are not limited to, f1-ori and colE1 ori.
The recombinant 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. Examples of suitable selectable markers include resistance genes against ampicillin (Ampr), tetracycline (Tcr), kanamycin (Kanr), phosphinothricin, and chloramphenicol (CAT) gene. 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).
Plants that have been stably transformed with a transgene encoding the dsRNA may be supplied as seed, reproductive material, propagation material or cell culture material which does not actively express the dsRNA but has the capability to do so.
Accordingly, the present invention encompasses a plant (e.g. a rice plant), or a seed (e.g. a rice seed), or a cell (e.g. a bacterial or plant cell), comprising any of the nucleotide sequences encoding the dsRNA or dsRNA construct as described herein. The present invention also encompasses a plant (e.g. a rice, barley, rye, wheat, miller, lovegrass or crabgrass plant), or a seed (e.g. a rice, barley, rye, wheat, miller, lovegrass or crabgrass seed), or a cell (e.g. a bacterial or plant cell), comprising any of the dsRNA or dsRNA constructs described herein. Preferably, these plants or seeds or cells comprise a recombinant construct wherein the nucleotide sequence encoding the dsRNA or dsRNA construct according to the present invention is operably linked to at least one regulatory element as described above. Preferably the plant or seed or cell is rice, or a rice seed or a rice cell.
General techniques for expression of exogenous double-stranded RNA in plants for the purposes of RNAi are known in the art (see Baulcombe D, 2004, Nature. 431(7006):356-63. RNA silencing in plants, the contents of which are incorporated herein by reference). 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 double-stranded RNA in plants for the purposes of down-regulating expression of a target gene in a plant pathogenic fungus. In order to achieve this effect it is necessary only for the plant to express (transcribe) the double-stranded RNA in a part of the plant which will come into direct contact with the fungus, such that the double-stranded RNA can be taken up by the fungus. Depending on the nature of the fungus and its relationship with the host plant, expression of the dsRNA could occur within a cell or tissue of a plant within which the fungus is also present during its life cycle, or the RNA may be secreted into a space between cells, such as the apoplast, that is occupied by the fungus during its life cycle. Furthermore, the dsRNA may be located in the plant cell, for example in the cytosol, or in the plant cell organelles such as a chloroplast, mitochondrion, vacuole or endoplastic reticulum.
Alternatively, the dsRNA may be secreted by the plant cell and by the plant to the exterior of the plant. As such, the dsRNA may form a protective layer on the surface of the plant.
In a further embodiment, the invention relates to a composition for controlling fungal growth and/or preventing or reducing fungal infestation, comprising at least one double-stranded RNA, wherein the double-stranded RNA comprises annealed complementary strands, one of which has a nucleotide sequence which is complementary to at least part of a nucleotide sequence of a fungal target gene and optionally further comprising at least one suitable carrier, excipient or diluent. The target gene may be any target gene described herein. Preferably the fungal target gene is essential for the viability, growth, development or reproduction of the fungus, for instance the fungal target gene is involved in any of the cellular functions as presented in Table 1; or the fungal target gene is involved in the pathogenicity or infectivity of the fungus, for instance the fungal target gene is involved in the formation of germ tubes, conidia attachment, formation of appressoria, formation of the penetration peg or formation of conidia.
In another aspect the invention relates to a composition as described above, wherein the fungal target gene comprises a sequence which is at least 75%, preferably at least 80%, 85%, 90%, more preferably at least 95%, 98% or 99% identical to a sequence selected from the group of sequences represented by any of SEQ ID NOs 3, 42, 99, 100, 527, 39, 60, 111, 112, 113, 114, 115, 116, 117, 536, 537, 538, 5, 43, 101, 102, 528, 1, 41, 97, 98, 526, 184, 185, 37, 59, 124, 9, 45, 106, 531, 188, 189, 13, 47, 109, 534, 33, 57, 126, 23, 52, 119, 35, 58, 127, 7, 44, 103, 104, 105, 529, 186, 187, 29, 55, 118, 17, 49, 108, 533, 25, 53, 121, 19, 50, 125, 31, 56, 123, 11, 46, 107, 532, 27, 54, 122, 21, 51, 120, 15, 48, 110, 535, 458, 486, 530, 460, 487, 539, 540, 462, 488, 541, 464, 489, 542, 466, 490, 543, 468, 491, 544, 470, 492, 545, 472, 493, 546, 474, 494, 547, 476, 496, 548, 478, 556, 549, 480, 497, 550, 482, 498, 551, 484, 499, 552 and 562 to 859, or the complement thereof, or wherein said fungal target gene is a fungal orthologue of a gene comprising any of SEQ ID NOs 3, 42, 99, 100, 527, 39, 60, 111, 112, 113, 114, 115, 116, 117, 536, 537, 538, 5, 43, 101, 102, 528, 1, 41, 97, 98, 526, 184, 185, 37, 59, 124, 9, 45, 106, 531, 188, 189, 13, 47, 109, 534, 33, 57, 126, 23, 52, 119, 35, 58, 127, 7, 44, 103, 104, 105, 529, 186, 187, 29, 55, 118, 17, 49, 108, 533, 25, 53, 121, 19, 50, 125, 31, 56, 123, 11, 46, 107, 532, 27, 54, 122, 21, 51, 120, 15, 48, 110, 535, 458, 486, 530, 460, 487, 539, 540, 462, 488, 541, 464, 489, 542, 466, 490, 543, 468, 491, 544, 470, 492, 545, 472, 493, 546, 474, 494, 547, 476, 496, 548, 478, 556, 549, 480, 497, 550, 482, 498, 551, 484, 499, 552 and 562 to 859.
The present invention further relates to a composition comprising at least one double-stranded RNA, at least one double-stranded RNA construct, at least one nucleotide sequence and/or at least one recombinant DNA construct as described herein, optionally further comprising at least one suitable 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 dsRNA by the fungal cell. 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 fungal cells, to substrates, to cells (e.g. plant cells), or to organism infected by or susceptible to infection by fungi.
It is contemplated that the “composition” of the invention may be supplied as a “kit-of-parts” comprising the double-stranded RNA in one container and a suitable diluent or carrier for the RNA in a separate container. The invention also relates to supply of the double-stranded RNA alone without any further components. In these embodiments the dsRNA 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 lyophilised 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 double-stranded RNAs, double-stranded RNA constructs, nucleotide sequences, recombinant DNA constructs, hairpin sequences or compositions described herein.
In one specific embodiment, the composition is a pharmaceutical or veterinary composition for treating or preventing fungal disease or infections of humans or animals, respectively. Such compositions will comprise at least one double-stranded RNA or RNA construct, or nucleotide sequence or recombinant DNA construct encoding the double-stranded RNA or RNA construct, wherein the double-stranded RNA comprises annealed complementary strands, one of which has a nucleotide sequence which corresponds to a target nucleotide sequence of a fungal target gene that causes the disease or infection, and at least one carrier, excipient or diluent suitable for pharmaceutical use.
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 composition to be applied to the skin as drops, gel, aerosol, or by brushing, or a spray, cream, ointment, etc. for topical application or as transdermal patches.
Alternatively, the fungal dsRNA is produced by bacteria (e.g. lactobacillus) which can be included in food and which functions as an oral vaccine against the fungal infection.
Other conventional pharmaceutical dosage forms may also be produced, including tablets, capsules, pessaries, transdermal patches, suppositories, etc. The chosen form will depend upon the nature of the target fungus and hence the nature of the disease it is desired to treat.
Preferred 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 or Aspergillus terreus group; Blastomyces dermatitidis; Paracoccidioides brasiliensis; Coccidioides immitis; Cryptococcus neoformans; Histoplasma capsulatum Var. capsulatum or Var. duboisii; Sporothrix schenckii; Fusarium spp.; Scopulariopsis brevicaulis and Fonsecaea spp.; Penicillium; Zygomycetes group of fungi, particularly Absidia corymbifera, Rhizomucor pusillus, and Rhizopus arrhizus.;
In animals: Candida spp.; Microsporum spp., particularly Microsporum canis, Microsporum gypseum; Trichophyton mentagrophytes; Aspergillus spp.; or Cryptococcus neoformans.
In one specific embodiment, the composition may be a coating that can be applied to a substrate in order to protect the substrate from infestation by a fungus and/or to prevent, arrest or reduce fungal growth on the substrate and thereby prevent damage caused by the fungus. 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 fungus, for example foodstuffs and other perishable materials, and substrates such as wood. Preferred target fungal species for this embodiment include, but are not limited to, the following: Stachybotrys spp., Aspergillus spp., Alternaria spp. or Cladosporium spp.
The nature of the excipients and the physical form of the composition may vary depending upon the nature of the substrate that 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 invention further encompasses a method for treating and/or preventing a fungal disease or condition, comprising administering to a subject in need of such treatment and/or prevention, any of the compositions as herein described, said composition comprising at least one double-stranded RNA or double-stranded RNA construct comprising annealed complementary strands, one of which has a nucleotide sequence which is complementary to at least part of a nucleotide sequence of a fungal target gene that causes the fungal disease or condition.
In another embodiment of the invention the compositions are used as a fungicide for a plant or for propagation or reproductive material of a plant, such as on seeds. As an example, the composition can be used as a fungicide by spraying or applying it on plant tissue or spraying or mixing it on the soil before or after emergence of the plantlets.
In yet another embodiment, the present invention provides a method for treating and/or preventing fungal growth and/or fungal infestation of a plant or propagation or reproductive material of a plant, comprising applying an effective amount of any of the compositions herein described to a plant or to propagation or reproductive material of a plant.
In another embodiment the invention relates to the use of transiently inserting dsRNA or RNA constructs, or a nucleotide sequence or recombinant DNA constructs encoding the double-stranded RNA or RNA construct described herein, in plants to treat fungi infested plants or plant fields. The transient transformation can for instance, but not necessarily, be established by modified plant virusses containing the appropriate nucleotide sequences to express fungus derived dsRNA in plants.
In another embodiment the invention relates to the use of any double-stranded RNA or RNA construct, or nucleotide sequence or recombinant DNA construct encoding the double-stranded RNA or RNA construct described herein, or to any of the compositions comprising the same, used for controlling fungal growth; for preventing fungal infestation of plants susceptible to fungal infection; or for treating fungal infection of plants. Specific plants to be treated for fungal infections caused by specific fungal species are as described earlier and are encompassed by the said use.
The invention further relates to a kit comprising at least one double-stranded RNA, or double-stranded RNA construct, or nucleotide sequence, or recombinant DNA construct, or cell, or composition as described earlier for treating fungal infection in plants. The kit may be supplied with suitable instructions for use. The instructions may be printed on suitable packaging in which the other components are supplied or may be provided as a separate entity, which may be in the form of a sheet or leaflet for example. The instructions may be rolled or folded for example when in a stored state and may then be unrolled and unfolded to direct use of the remaining components of the kit.
According to a still further embodiment, the present invention extends to a method for increasing plant yield comprising introducing in a plant any of the nucleotide sequences or recombinant DNA constructs as herein described in an expressible format. Plants encompassed by this method are as described earlier. Preferably, said plant is rice.
In one 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 fungal genes by RNAi can be used in in vitro or in vivo assays in order to study gene function, in an analogous approach to that which has been described in the art for the nematode worm C. elegans and also Drosophila melanogaster. Assays based on targeted down-regulation of specific fungal genes, leading to a measurable phenotype may also form the basis of compound screens for novel anti-fungal agents.
FIGS. 3A-3MM: List of target genes including the coding sequences. The start and stop codons are at the beginning and at the end of the underlined sequence.
Table 1: Examples of suitable fungal target genes. The DNA and protein sequences given in the table originate from the rice blast fungus Magnaporthe grisea (also known as Magnaporthe oryzae). Identifiers correspond to the gene identifiers of the M. grisea genome project. The homologous genes of the budding yeast Saccharomyces cerevisiae are also given, identifiers correspond to gene identifiers of the Saccharomyces Genome Database (SGD™), together with gene function assigned on the basis of yeast data.
Table 2: Examples of suitable fungal target genes. The DNA and protein sequences given in the table correspond with fungal orthologues of the rice blast fungus Magnaporthe grisea genes of Table 1. Identifiers correspond to accession number and version number.
Table 3: Overview of cloning details of (A) cDNA's of Magnaporthe grisea target genes and (B) fragments. PCR conditions were as follows: A: Expand High Fidelity PCR system (Roche) 5′ 94° C., 30 cycles (1′ 94° C., 1′ 58° C., 1′ 72° C.) 10′ 72° C.; B: Expand High Fidelity PCR system (Roche) 5′ 94° C., 30 cycles (45″ 94° C., 45″ 58° C., 45″ 72° C.), 10′ 72° C.; C: Expand High Fidelity PCR system (Roche) 5′ 94° C., 30 cycles (45″ 94° C., 45″ 58° C., 45″ 72° C.), 10′ 72° C.; D: Expand High Fidelity PCR system (Roche) 5′ 94° C. 30 cycles (1′ 94° C., 1′ 60° C., 3′ 72° C.), 5′ 72° C.; E: Taq Polymerase (Bangalore Genei) 3′ 95° C., 10 cycles (30″ 95° C., 30″ 55° C., 3′ 72), 25 cycles (30″ 95° C., 30″ 55° C., 3′(+5″/cycle) 72), 7′ 72° C.; and F: GC Polymerase (BD Biosciences) 5′ 94° C., 30 cycles (1′ 94° C., 1′ 58° C., 3′ 68° C.) 10′ 68° C.; G: RedTaq polymerase (Sigma) 2′ 94° C., 33 cycles (2′ 94° C., 30″ 56° C., 30″ 72° C.) 10′ 72° C.
Table 4: Overview of cloning details of exons of Magnaporthe grisea target genes using gDNA as template. PCR conditions were as follows: A: Pwo polymerase (Roche) 5′ 94° C., 30 cycles (30″ 94° C., 30″ 60° C., 1′ 72° C.) 5′ 72° C.; B: Pwo polymerase (Roche) 5′ 94° C., 30 cycles (30″ 94° C., 30″ 58° C., 30″ 72° C.) 5′ 72° C.; C: Pwo polymerase (Roche) 5′ 94° C., 30 cycles (1′ 94° C., 1′ 61° C., 1′30″ 72° C.) 5′ 72° C.; D: Pwo polymerase (Roche) 5′ 94° C., 30 cycles (30″ 94° C., 30″ 60° C., 30″ 72° C.) 5′ 72° C.; E: Pwo polymerase (Roche) 5′ 94° C., 30 cycles (45″ 94° C., 45″ 60° C., 45″ 72° C.) 5′ 72° C.; F: Pwo polymerase (Roche) 10′ 94° C., 30 cycles (1′ 94° C., 1′ 60° C., 3′ 72° C.) 10′ 72° C.
Table 5A and 5B: Selected target nucleotide sequences of the fungal target genes: (IV) stands for experiments in vitro done, (PE) for plant expression experiments and * are ongoing experiments in vitro.
Table 6: Primers used for hairpin construction in pMH115
Table 7: Sporulation phenotype in the presence of 1 or 2 μM dsRNA of targets and negative controls (Seastar and GST) at 4 days. “−” indicates a >90% reduction, “+/−” indicates a 80-90% reduction, “+” indicates a 75-80% reduction in spore formation. “+++” indicates untreated or negative control dsRNA-treated level of spores formed.
Table 8: Selected sequences* of target genes. Fragments of at least 17 bp of the sequences* are present in any of the orthologues sequences in fungi species (represented by GI number in the right column; several database entry numbers were found but only one is given by way of example).
Table 9: Selected sequences* of target genes. Fragments of at least 17 bp of the sequences* are present in any of the orthologues sequences in nematode species (represented by GI number in the right column; several database entry numbers were found but only one is given by way of example).
Table 10: Selected sequences* of target genes. Fragments of at least 17 bp of the sequences* are present in any of the orthologues sequences in insect species (represented by GI number in the right column; several database entry numbers were found but only one is given by way of example).
The invention will be further understood with reference to the following non-limiting examples.
The methods for dsRNA mediated gene silencing in fungi as described herein are applicable to combat plant pathogenic fungi with dsRNA corresponding to a plant pathogen target gene. Suitable plant pathogen target genes were identified and isolated from the fungus as follows.
Total RNA was prepared from the fungus Magnaporthe grisea using the RNEASY® (RNA purification) Mini kit for plants (QIAGEN Cat. No. 74904), from which cDNA was prepared using the SUPERSCRIPT® (reverse transcriptase) Double-Stranded cDNA synthesis kit (Invitrogen). To isolate the coding sequence of the Magnaporthe grisea target genes MG00884.4, MG04484.4, MG07472.4, MG06292.4, MG03668.4, MG05169.4 and MG03872.4, PCRs were performed on the Magnaporthe grisea cDNA or on genomic DNA as a template.
The PCR conditions and primers for the target gene are outlined in the tables. Each PCR was performed in duplicate. The resulting two independent PCR products per target gene, were analysed on agarose gel, isolated and cloned into the pTZ57R/T vector (MBI Fermentas). For each PCR product, at least three clones were sequenced. The sequences resulting from the clones were compared to the public database sequences and one or more clones per target gene were selected for further experimentation. Cloning details of the coding sequences of these genes are herein represented in the tables.
To isolate fragments of the Magnaporthe grisea target genes, total RNA was extracted from Magnaporthe grisea mycelium (RNEASY® (RNA purification) Plant Mini kit, Qiagen). A reverse transcription reaction (SUPERSCRIPT® II (reverse transcriptase), Invitrogen) was done on the total RNA to produce the first strand cDNA, which was then used to amplify partial or full cDNA of target fragments. The cDNA's were cloned into a TOPO® (topoisomerase) TA vector (Invitrogen), and the constructs were used as templates to synthesize dsRNA from (T7 RIBOMAX™ kit (in vitro transcription system), Promega).
Seastar AFP (autofluorescent protein) template was an in-house clone pGR37, Glutathione S-transferase (GST) was amplified from pGEX4T-1, GFP was amplified from an in-house clone, pDW2821. Exons of beta-tubulin genes were amplified directly from gDNA and used as templates for dsRNA synthesis.
Alternative Cloning: Cloning of Exons of cDNA:
For cDNA's that could not be amplified from total RNA, exons were amplified from genomic DNA (gDNA) and the exons ligated together to form the cDNA. Genomic DNA of Magnaporthe grisea was prepared using a protocol modified from Naqvi et al. (Molecular Breeding, 1995, 1: 341-348). About 150 mg of dried mycelium was ground in liquid nitrogen into powder form and extracted for genomic DNA in extraction buffer (10 mM Tris pH 8.0, 1 mM EDTA, 0.25 M NaCl, 1% SDS) at 65° C. for 30′. Cell debris and proteins were precipitated by adding potassium acetate 5 M pH 4.8 at −20° C. freezer for 15′. The pellet was removed by centrifugation at 14000 rpm for 10′. The supernatant was transferred to a fresh tube and extracted with phenol/CH3Cl/isoamyl alcohol mix. The aqueous layer was precipitated with isopropanol. The DNA pellet was washed with 70% ethanol, air-dried and resuspended in TE. This preparation is used as template for amplification of exons by PCR of the following fungal target genes.
To isolate the coding region of the Magnaporthe grisea target genes MG00170.4, MG07031.4, MG02946.4 and MG10192.4, two independent PCRs were performed for each exon of each target gene. The full length genomic gene sequence amplified from gDNA was used as template for amplifying each of the exons to compile the cDNA comprising the coding region. The PCR conditions for each exon of the target genes are outlined in Table 4. Subsequently, to obtain the full length coding sequence, the amplified exons/PCR products originating from the same target were analyzed on agarose gel, isolated, and ligated to each other in the correct order. This ligation was achieved as follows:
Step 1: PCR amplification of each exon using the proof reading enzyme Pwo polymerase (Roche), producing blunt ends.
Step 2: Phosphorylation of 2.5 pmols of the second exon using 1 unit of Polynucleotide kinase (PNK, Bangalore Genei) in a 15 μl reaction with 1 mM ATP.
Step 3: Blunt end ligation of the two exons.
Step 4: PCR amplification of the full-length gene from the ligation mix using gene specific forward and reverse primers. This step ensures selection of only those ligation products in which the exons are ligated in the correct order.
In case of target gene MG07031.4 (3), which has 5 exons, the first two exons (Exon 1 and 2 which were 70 bp and 21 bp respectively) were synthetically made. The last 3 exons were amplified as outlined hereinabove and ligated as follows:
The ligation products were cloned into the pTZ57R/T vector (MBI Fermentas). For each ligation product, at least 3 clones were sequenced. The sequences resulting from the clones were compared to the public database sequences and one or more clones per target gene were selected for further experimentation. Cloning details of exons which are joined to form the coding sequences of these target gens are herein represented in Table 4. cDNA's of the other target genes were cloned by one of the above approaches.
The beta-tubulin was used to optimize the size of fragments that give color effect in the color assay (Example 4.3). 200, 400 and 600 bp fragments from the 3′ end of the coding region were tested in the color assay and a 400 bp, E7F7 (
Fragments of the target genes herein described were selected for use in further RNAi experiments both in vitro as described in example 4 or in vivo as described in examples 5, 6 and 7. These fragments are listed in Table 5. (PY maybe A person skilled in the art will recognize that other fragments of various lengths may be identified in the Magnaporthe grisea sequences, and that the present invention also extends to these fragments and the use thereof in RNAi mediated silencing of fungal genes.
These fragments or target nucleotide sequences of fungal target genes were used to produce dsRNA in vitro as is described in example 4, or were cloned in a hairpin construct to produce dsRNA in a plant cell (see example 5).
Germinating conidia have been shown to actively take up materials from the medium by endocytosis. In the following assay germinating conidia of Magnaporthe grisea were used to demonstrate uptake of dsRNA by fungi in vitro. Conidia were germinated in hydrophilic conditions, mimicking their germination within the leaf after penetration of the fungus. On a hydrophilic surface, the conidia grow vegetatively into mycelia.
dsRNA corresponding to target regions of target genes were prepared from genomic DNA or cDNA as follows. Two PCR reactions were set up: one to amplify the sense RNA strand, another for the antisense RNA strand. The forward primers of each reaction contain a T7 promoter sequence followed by sequences corresponding to the targeted sequence, while the reverse primer only contains sequence complementary to the target sequence. The PCR products were purified using the QIAQUICK® PCR Purification Kit (for DNA purification) (Qiagen), and subsequently used as template for in vitro transcription to produce double-stranded RNA (T7 RIBOMAX™ Express RNAi System (in vitro transcription system) Promega). The dsRNA was precipitated, quantitated and dissolved in RNase-free water.
Conidia (asexual spores) were generated by exposing fungal mycelia to light for 7-10 days. Freshly harvested, hydrated conidia were re-suspended in water at a density of 104 conidia/ml, and inoculated on the hydrophobic surface of an artificial membrane (GELBOND® film (plastic film adapted to support a gel coating), Cambrex). DsRNA corresponding to the respective fungal target genes (see Table 5) were tested individually at concentrations ranging from 0.1-1 mg/ml in a final volume of 20 μl in water. As a negative control, dsRNA corresponding to part of a GST was used. After 16-24 h incubation at 28° C., the germinated spores were stained with Acid Fuchsin for clearer visualization of cellular structures.
Formation of appressoria on the artificial membrane was observed under a microscope. The inhibition of germ tube and appressorium formation was a direct indication of inhibition of target gene expression by RNAi due to uptake of dsRNA by the intact fungus. Soaking experiments were performed in triplicate. The percentage of appressoria formed was calculated by the number of appressoria divided by the number of spores in 3 given fields in the microscope and at least 200 spores were counted per replicate.
Conidia of Magnaporthe grisea were harvested, re-suspended in potato dextrose broth and 1250 conidia (in about 90 μl) were aliquoted in each well of a hydrophilic 96-well plates (Falcon 3072). After 0-2 h pregermination at 28° C., dsRNA was added to a final volume of 100 μl and to a final concentration of 0.1 or 0.5 mg/ml. dsRNA fragments of about 200 bp in length corresponding to distinct target regions of the target genes were tested. As negative controls, dsRNA corresponding to a part of GST, Seastar AFP or GFP were used. After 16-24 h incubation at 28° C., the growth of mycelia in the wells was quantified by optical density reading of the 96-well plates at wavelength 595 nm, in a plate reader (GENios Tecan, Austria). The fungus showed growth inhibition in the presence of target dsRNA fragments compared to controls (see Table 5 and
Unless otherwise stated, spores from B157, an Indian isolate of Magnaporthe grisea strain (Naqvi N, personal communication) were used. Spores were generated after exposing mycelium to light for 9-11 days, were harvested and used fresh or frozen. Fresh and frozen spores behaved similarly in this assay (data not shown). For consistency, a single frozen stock was used in all assays reported here. The spores were diluted in PDBM (potato dextrose buffer with 25 mM MES buffer pH 5.5) before aliquoting into the wells of a 96-well plate to give 1250 spores per well.
Various amounts of dsRNA were added to spores in the wells and mixed well. The final volume was made up to 100 μl with PBDM. The plates were incubated at 28° C. in the dark and the color was recorded with a digital camera at 7 days. Spores from two Magnaporthe grisea isolates, R67 (
As a separate readout of RNAi effect of contacting dsRNA to spores, the sporulation phenotype was observed. In a similar assay set up as described above, the spores were incubated with dsRNA in 96 or 48 well plates. In contrast to the assay above, the plates were exposed to continuous light to induce spore formation and the plates were incubated at 26° C. At day 4-6, the extent of spore formation is viewed under a Nikon microscope and pictures taken with a Nikon digital camera (
Since the mechanism of RNA interference operates through dsRNA fragments, the target nucleotide sequences of the target genes as selected above and indicated in Table 5 were cloned in anti-sense and sense orientation, separated by the 189 bp synthetic intron (SI) from the gene X from Arabidopsis thaliana (SI, SEQ ID NO: 204), to form a dsRNA hairpin construct. These hairpin constructs were cloned into multiple cloning sites of the plant expression vector pMH115 (SEQ ID NO: 205), comprising the double CaMV35S promoter and the CaMV35S 3′ element. The cDNA clones as described above were used as templates for the PCRs. These cloning experiments resulted in a hairpin construct for each target gene, having the structure promoter-sense-SI-antisense or more preferably, promoter-antisense-SI-sense, wherein the sense fragments are given in Table 5, and wherein the promoter is any plant operable promoter, preferably a strong constitutive promoter, such as the CaMV35S promoter. The complete sequences of several hairpin constructs (antisense- SI-sense) are represented in
The hairpin constructs as described above were embedded in the binary vector pMH115 with the double CaMV35S promoter, which vector is suitable for transformation into A. tumefaciens, transformation into rice, and expression of the hairpin in rice.
Alternatively, other vectors are used for transformation and other promoters are used for expression of the hairpin dsRNA for the target genes herein described. For example, such promoters are selected from strong constitutive promoters including strong constitutive promoters such as CaMV35S promoter, doubled CaMV35S promoter, ubiquitin promoter, actin promoter, rubisco promoter, GOS2 promoter and FMV promoter.
The plant expression vectors comprising the Magnaporthe grisea hairpins were subsequently transformed into in Agrobacterium tumefaciens (see example 6).
Rice calli were transformed and regenerated into shoots and whole plants as described in literature. The plants were transferred to a greenhouse and cultivated to reach maturity and to set seeds. Genomic PCR and/or Southern blotting is performed on leaf tissue of T1 plants to determine the homozygosity/heterozygosity of the integrated locus and the number of inserted copies of transgene. Transgene-positive plants are further analyzed by Northern blotting and/or RT-PCR to detect expression of dsRNA and siRNA. Homozygous lines showing expression of dsRNA and/or siRNA are established and used for fungal infection studies.
Explants (15-20 replicates each) from T1 plants (both heterozygous and homozygous integrants) are used for initial analysis of resistance to rice blast infection. The leaves of 20 day-old plants are cut and the ends of the leaves are inserted into kinetin agar plates. A small drop of Magnaporthe grisea spores (200-1000 spores in 20 μl water) are inoculated onto the leaves. Infection rate and lesion sizes are compared between test and negative control leaves.
In planta infection of established dsRNA-expressing strains are sprayed with fungal spores of 105/ml density, and then covered with plastic bags perforated with holes. These plants are maintained in environmental chambers (Convirons) until disease symptoms develop. The timing of appearance, size and number of lesions, and the rate of plant wilting are indicators of susceptibility to Magnaporthe grisea infection (Valent B. 1990. Phytopathology 80: 57-67). Fifty to 100 replicates per transformed line are used in each experiment. Resistant rice strains are further tested in Convirons as well as in field conditions.
It will be appreciated by persons skilled in the art that numerous variations and/or modifications may be made to the invention as shown in the specific embodiments without departing from the spirit or scope of the invention as broadly described. The present embodiments are, therefore, to be considered in all respects as illustrative and not restrictive.
Furthermore, throughout this specification the word “comprise”, or variations such as “comprises” or “comprising”, will be understood to imply the inclusion of a stated element, integer or step, or group of elements, integers or steps, but not the exclusion of any other element, integer or step, or group of elements, integers or steps.
Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments of the invention described herein. Such equivalents are intended to be encompassed by the following claims.
All references, including patent documents, disclosed herein are incorporated by reference in their entirety.
S.
cerevisiae
M. grisea identifier
Gibberella zeae PH-1
Aspergillus fumigatus
Candida glabrata
Aspergillus niger
Candida albicans
Paracoccidioides brasiliensis
Mycosphaerella graminicola
Aspergillus nidulans FGSC A4
Sclerotinia sclerotiorum
Cryptococcus neoformans var.
Ustilago maydis
Blumeria graminis f. sp.
Aspergillus flavus
Phytophthora infestans
Fusarium sporotrichioides
Fusarium oxysporum f. sp.
Magnaporthe grisea 70-15
Candida albicans
Botryotinia fuckeliana
Paracoccidioides brasiliensis
Phaeosphaeria nodorum
Aspergillus niger
Phytophthora parasitica
Phytophthora infestans
Phytophthora parasitica
Aspergillus flavus
Verticillium dahlias
Fusarium sporotrichioides
Fusarium sporotrichioides
Alternaria brassicicola
Conidiobolus coronatus
Blumeria graminis f. sp.
Fusarium oxysporum f. sp.
Pythium ultimum
Leptosphaeria maculans
Trichophyton rubrum
Erysiphe pisi
Magnaporthe grisea 70-15
Gibberella zeae PH-1
Ustilago maydis
Aspergillus nidulans FGSC A4
Candida glabrata
Cryptococcus neoformans var.
Aspergillus fumigatus
Botryotinia fuckeliana
Aspergillus flavus
Candida albicans
Candida albicans
Cryptococcus neoformans var.
Ustilago maydis
Mycosphaerella graminicola
Aspergillus niger
Paracoccidioides brasiliensis
Phytophthora sojae
Phytophthora infestans
Magnaporthe grisea 70-15
Gibberella zeae PH-1
Aspergillus nidulans FGSC A4
Aspergillus fumigatus
Aspergillus fumigatus
Aspergillus fumigatus
Aspergillus nidulans FGSC A4
Aspergillus niger
Aspergillus flavus
Mycosphaerella graminicola
Paracoccidioides brasiliensis
Ustilago maydis
Candida glabrata
Magnaporthe grisea 70-15
Gibberella zeae PH-1
Gibberella zeae PH-1
Aspergillus nidulans FGSC A4
Aspergillus niger
Aspergillus niger
Aspergillus fumigatus
Ustilago maydis
Paracoccidioides brasiliensis
Cryptococcus neoformans var.
Candida albicans
Phytophthora infestans
Magnaporthe grisea 70-15
Cryptococcus neoformans var.
Candida glabrata
Candida albicans
Paracoccidioides brasiliensis
Verticillium dahlias
Aspergillus niger
Mycosphaerella graminicola
Alternaria brassicicola
Phytophthora sojae
Phytophthora infestans
Magnaporthe grisea 70-15
Gibberella zeae PH-1
Ustilago maydis
Aspergillus nidulans FGSC A4
Aspergillus fumigatus
Gibberella zeae PH-1
Aspergillus fumigatus
Aspergillus flavus
Candida albicans
Ustilago maydis
Magnaporthe grisea 70-15
Aspergillus nidulans FGSC A4
Aspergillus fumigatus
Aspergillus flavus
Paracoccidioides brasiliensis
Candida albicans
Alternaria brassicicola
Cryptococcus neoformans var.
Magnaporthe grisea 70-15
Gibberella zeae PH-1
Aspergillus fumigatus
Aspergillus nidulans FGSC A4
Ustilago maydis
Candida albicans
Botryotinia fuckeliana
Fusarium sporotrichioides
Fusarium sporotrichioides
Cryptococcus neoformans var.
Magnaporthe grisea 70-15
Gibberella zeae PH-1
Magnaporthe grisea 70-15
Gibberella zeae
Gibberella zeae PH-1
Aspergillus flavus
Aspergillus nidulans FGSC A4
Aspergillus flavus
Aspergillus niger
Aspergillus fumigatus
Ustilago maydis
Paracoccidioides brasiliensis
Leptosphaeria maculans
Botryotinia fuckeliana
Mycosphaerella graminicola
Verticillium dahlias
Phytophthora sojae
Phytophthora infestans
Candida albicans
Alternaria brassicicola
Cryptococcus neoformans var.
Phytophthora parasitica
Blumeria graminis f. sp.
Candida glabrata
Candida albicans
Ustilago maydis
Paracoccidioides brasiliensis
Cryptococcus neoformans var.
Botryotinia fuckeliana
Magnaporthe grisea 70-15
Gibberella zeae PH-1
Aspergillus nidulans FGSC A4
Aspergillus fumigatus
Emericella nidulans
Aspergillus fumigatus
Cryptococcus neoformans var.
Candida albicans
Candida albicans
Ustilago maydis
Aspergillus flavus
Paracoccidioides brasiliensis
Magnaporthe grisea 70-15
Gibberella zeae PH-1
Gibberella zeae PH-1
Gibberella zeae PH-1
Aspergillus nidulans FGSC A4
Aspergillus fumigatus
Candida glabrata
Paracoccidioides brasiliensis
Ustilago maydis
Cryptococcus neoformans var.
Phytophthora parasitica
Magnaporthe grisea 70-15
Magnaporthe grisea 70-15
Gibberella moniliformis
Gibberella zeae
Aspergillus niger
Aspergillus fumigatus
Botryotinia fuckeliana
Paracoccidioides brasiliensis
Aspergillus flavus
Candida glabrata
Aspergillus nidulans FGSC A4
Candida albicans
Fusarium sporotrichioides
Ustilago maydis
Cryptococcus neoformans var.
Phanerochaete chrysosporium
Phytophthora parasitica
Phytophthora infestans
Phytophthora parasitica
Alternaria brassicicola
Candida albicans
Paracoccidioides brasiliensis
Ustilago maydis
Magnaporthe grisea 70-15
Gibberella zeae PH-1
Aspergillus nidulans FGSC A4
Aspergillus fumigatus
Aspergillus fumigatus
Aspergillus nidulans FGSC A4
Paracoccidioides brasiliensis
Candida glabrata
Ustilago maydis
Cryptococcus neoformans var.
Candida albicans
Magnaporthe grisea 70-15
Gibberella zeae PH-1
Gibberella zeae PH-1
Aspergillus fumigatus
Aspergillus nidulans FGSC A4
Botryotinia fuckeliana
Cryptococcus neoformans var.
Aspergillus niger
Aspergillus flavus
Ustilago maydis
Phytophthora infestans
Paracoccidioides brasiliensis
Candida albicans
Magnaporthe grisea 70-15
Gibberella zeae PH-1
Aspergillus fumigatus
Aspergillus nidulans FGSC A4
Botryotinia fuckeliana
Cryptococcus neoformans var.
Paracoccidioides brasiliensis
Candida glabrata
Magnaporthe grisea 70-15
Aspergillus fumigatus
Fusarium sporotrichioides
Aspergillus flavus
Aspergillus niger
Candida glabrata
Magnaporthe grisea 70-15
Gibberella zeae PH-1
Ustilago maydis
Candida albicans
Candida albicans
Aspergillus niger
Verticillium dahliae
Botryotinia fuckeliana
Fusarium sporotrichioides
Cryptococcus neoformans var.
Fusarium oxysporum f. sp.
Phaeosphaeria nodorum
Conidiobolus coronatus
Cladosporium fulvum
Paracoccidioides brasiliensis
Mycosphaerella graminicola
Phytophthora infestans
Magnaporthe grisea 70-15
Gibberella zeae PH-1
Aspergillus nidulans FGSC A4
Aspergillus fumigatus
grisea identifer
This application is a divisional of U.S. application Ser. No. 12/778,278, filed May 12, 2010, which is a divisional of U.S. application Ser. No. 11/396,926, filed Apr. 3, 2006, which is a continuation-in-part of PCT/IB2005/003495, filed Oct. 4, 2005, which claims the benefit under 35 U.S.C. §119(e) of U.S. provisional application 60/615,695, filed Oct. 4, 2004, the entire disclosures of which are incorporated herein by reference.
| Number | Date | Country | |
|---|---|---|---|
| 60615695 | Oct 2004 | US |
| Number | Date | Country | |
|---|---|---|---|
| Parent | 12778278 | May 2010 | US |
| Child | 14488493 | US | |
| Parent | 11396926 | Apr 2006 | US |
| Child | 12778278 | US |
| Number | Date | Country | |
|---|---|---|---|
| Parent | PCT/IB2005/003495 | Oct 2005 | US |
| Child | 11396926 | US |
