WO1995022245A1 - Antiviral transgenic plants, vectors, cells and methods - Google Patents
Antiviral transgenic plants, vectors, cells and methods Download PDFInfo
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- WO1995022245A1 WO1995022245A1 PCT/US1995/002058 US9502058W WO9522245A1 WO 1995022245 A1 WO1995022245 A1 WO 1995022245A1 US 9502058 W US9502058 W US 9502058W WO 9522245 A1 WO9522245 A1 WO 9522245A1
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- Prior art keywords
- plant
- leu
- lys
- glu
- transgenic
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Classifications
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
- C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
- C12N15/09—Recombinant DNA-technology
- C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
- C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
- C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
- C12N15/8241—Phenotypically and genetically modified plants via recombinant DNA technology
- C12N15/8261—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield
- C12N15/8271—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield for stress resistance, e.g. heavy metal resistance
- C12N15/8279—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield for stress resistance, e.g. heavy metal resistance for biotic stress resistance, pathogen resistance, disease resistance
- C12N15/8283—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield for stress resistance, e.g. heavy metal resistance for biotic stress resistance, pathogen resistance, disease resistance for virus resistance
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
- C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
- C12N9/14—Hydrolases (3)
- C12N9/16—Hydrolases (3) acting on ester bonds (3.1)
- C12N9/22—Ribonucleases RNAses, DNAses
Definitions
- the present invention relates to isolated 2-5A-dependent RNases having the ability to bind 2-5A and/or cleave single stranded RNA when bound to 2-5A, encoding sequences therefor, recombinant nucleotide molecules, recombinant vectors, recombinant cells, and antiviral transgenic plants which express, for example, antiviral animal amino acid sequences which have activity similar or identical to 2-5A-dependent RNase, 2-5A synthetase and/or PKR.
- RNA degradation is a critical cell function, and gene expression is often regulated at the level of RNA stability. See, e.g., Shaw, G and Ka en, R., Cell. 46:659-667 (1986). Nonethe less, relatively little is known about the bio chemical pathways that mediate RNA degradation i mammalian or plant systems. For instance, most i not all of the ribonucleases responsible for mRN turnover in mammalian or plant cells remai unidentified. This was reviewed in Brawerman, G. Cell. 57:9-10 (1989).
- the 2-5A system is believed t be the only well-characterized RNA degradatio pathway from higher animals including man. See FIG 1. See also, e.g., Kerr, I.M. and Brown, R.E., Prod Natl. Acad. Sci. U.S.A.. 75:256-260 (1978) an Cayley, P.J. et al., Biophvs Res. Commun. 108:1243-1250 (1982); reviewed in Sen, G.C. an Lengyel, P., J. Biol. Chem.. 267:5017-5020 (1992)
- the activity of the 2-5A system is believed to b mediated by an endoribonuclease known as 2-5A dependent RNase.
- 2-5A-dependen RNase is a unique enzyme in that it requires 2-5A unusual oligoadenylates with 2',5' phosphodieste linkages, p n (A2 p) n A, for ribonuclease activity.
- 2-5A is produced from AT by a family of synthetases in reactions requirin double-stranded RNA (dsRNA) . See FIG. 1. See als Hovanessian, A.G. et al.. Nature. 268:537-539 (1977) Marie, I. and Hovanessian, A.G., J. Biol. Chem. 267:9933-9939 (1992). 2-5A is unstable in cells an in cell-free systems due to the combined action o 2',5 '-phosphodiesterase and 5'-phosphatase.
- 2-5A-dependent RNase i believed to have no detectable RNase activity unti .it- " is converted to its active state by binding t 2-5A. See Silverman, R.H. , Anal. Biochem. 144:450-460 (1985). Activated 2-5A-dependent RNas cleaves single-stranded regions of RNA 3' of UpNp with preference for UU and UA sequences. Se Wreschner, D.H. et al.. Nature. 289:414-417 (1981a) and Floyd-Smith, G. et al.. Science. 212:1020-103 (1981) .
- Interferons ⁇ , ⁇ or Y are believed to induce the accumulation of both 2-5A-dependent RNase, Jacobsen, H. et al.. Virology. 125:496-501 (1983A) and Floyd-Smith, G. , J. Cellular Biochem.. 38:12-21 (1988) , and 2-5A synthetases, Hovanessian, A.G. et al.. Nature, 268:537-539 (1977), reviewed in Sen, G.C. and Lengyel, P., J. Biol. Chem..
- the 2-5A system however, almost certainl provides functions beyond the antipicornaviru activity of interferons.
- introductio of 2-5A into cells Hovanessian, A.G. and Wood, J.N. Virology. 101:81-90 (1980), or expression of 2-5 synthetase cDNA, Rysiecki, G. et al., J. Interfero Res.. 9:649-657 (1989)
- 2-5A-dependent RNase levels are elevated i growth arrested cells, Jacobsen, H. et al., Proc Natl. Acad. Sci. U.S.A..
- PKR dsRNA-dependent protein kinase enzyme
- PKR dsRNA-dependent protein kinase enzyme
- PKR is stimulated by dsRNA.
- activated PKR phosphorylates the alpha subunit of translation factor eIF 2 , known as eIF 2 -alpha, which indirectly inhibits protein synthesis initiation.
- interferons ⁇ , f and ⁇ induce the accumulation of PKR. See Hoavanessian et al.: J. Interferon Res.. 9:641-647 (1989).
- the PKR system is also likely to provide functions beyond the antipicornavirus activity of interferons. See Meurs, E.F. et al.: J. Virolo ⁇ v. 66:5805-5814 (1992). For example, expression of mutant forms of PKR in NIH 3T3 cells resulted in tumor formation when injected into nude mice. See Meurs, E.F. et al. : Proc. Natl. Acad. Sci U.S.A.. 90:232-236 (1993).
- the 2-5A system and the PK system inhibit viral protein synthesis. This is believed to be accomplished by the 2-5A system b degrading mRNA and rRNA whereas the PKR system i believed to accomplish this by indirectly inhibitin protein synthesis initiation.
- Viral plant diseases are pandemic and thei severity varies from mild symptoms to plant death. The majority of plant viruses are believed to hav single stranded RNA genomes. Moreover, it i currently believed that plants are void of the thre enzymes discussed above, i.e., PKR, 2-5A synthetas and 2-5A-dependent RNase. See Cayley, P.J. et al.: Biochem. Biophvs Res. Commun... 108:1243-1250 (1982) and Devash, Y. et al.: Biochemistry. 24:593-59 (1985); but see Crum, C. et al.: J. Biol. Chem..
- the present invention alleviates and overcomes certain of the above-mentioned problems and shortcomings of the present state of the art through the discovery of novel, isolated 2-5A-dependent RNases and encoding sequences therefor.
- the novel 2-5A dependent RNases of the instant invention are involved in the fundamental control of single stranded RNA decay in animal cells, such as mammals, and are also present in animal cells, such as avian and reptilian cells. More particularly, the novel 2-5A dependent RNases of the " present invention have the ability to degrade single stranded RNA, mainly 3' of UpUp or UpAp sequences, after they are activated by binding to 5'-phosphorylated,2',5'-linked oligoadenylates (hereinafter "2-5A") . As a result, it is believed that the novel 2-5A dependent RNases are useful in connection with inhibition of cell growth rates, viral replication and in connection with interferon treatment of viral infection and cancer.
- 2-5A 5'-phosphorylated,2',5'-linked oligoadenylates
- H 2-5A-dependent RNase(s) is used in a broad sense and is meant to include any amino acid sequence which includes a 2-5A binding domain and/or ribonuclease function when the 2-5A-dependent RNas is activated by 2-5A.
- the novel 2-5A dependent RNases of th present invention are protein enzymes havin molecular weights on the order of between about 7 KDa (murine) and about 84 KDa (human) , as determine by gel electrophoresis migration and/or predictio from their respective encoding nucleotide sequences
- a human 2-5A-dependent RNase of th instant invention has a molecular weight of abou 83,539 Da as determined from the amino acid sequenc predicted from the encoding sequence therefor whereas the murine 2-5A-dependent RNase has molecular weight of about 74 KDa as determined by ge electrophoresis migration and from prediction of th amino acid sequence from the encoding sequence
- an about 74 KDa molecular weight is reporte herein for a murine 2-5A-dependent RNase, it shoul nevertheless be appreciated that the reporte molecular weight is for an incomplete murin 2-5A-dependent RNase.
- the amino acid sequence for human 2-5A-dependent RNase protein is depicted in FIG. 3 and Table 1.
- the encoding sequence for the human 2-5A-dependent RNase protein is also set forth in Table 1.
- the mRNA for human 2-5A-dependent RNase is about 5.0 Kb in size.
- the mRNA for murine 2-5A-dependent RNase is about 5.7 Kb in size.
- the novel 2-5A dependent RNases of the instant invention include the following uniqu domains which span between the amino terminus and the carboxy terminus. For instance, it has bee discovered that there are at least four and possibl as many as nine or more ankyrin repeats, of whic three lie closest to the amino terminus.
- ankyrin repeats there may be additional ankyri repeats that may total, for instance, about eight o more when the amino acid sequences of th 2-5A-dependent RNases of the present invention ar further analyzed. It is believed that these ankyri repeats may possibly function in protein-protei interaction.
- Ankyrin repeat 1 generally lies betwee amino acids designated as 58-90 in Tables 1 and 2
- Ankyrin repeat 2 generally lies between amino acid designated as 91-123 in Tables l and 2 •
- Ankyri repeat 3 generally lies between amino acid designated as 124-156 in Tables i and 2•
- Ankyri repeat 4 generally lies between amino acid designated as 238 and 270 in Tables ⁇ and 2 • Se also FIGS. 10A and 10B.
- the nove 2-5A dependent RNases include a cysteine rich regio (which has homology to zinc fingers) that lies close to the carboxy terminus than the amino terminus whic may possibly function in RNA recognition or i formation of protein dimers.
- the cysteine ric region is believed to include about 5 or 6 cystein residues which generally lie between amino acid designated as 395-444 in the human sequence a reported in Table 1 and FIG. 4, or between amin acids designated as 401-436 in the murine sequence a reported in Table 2 and FIG. 4.
- the novel 2-5A dependent RNases include a duplicated phosphate binding (2 P-loops) motif which lies generally within the ankyrin repeat motifs.
- each P-loop motif includes a lysine residue which is essential for maximum 2-5A binding activity.
- the lysine residues are designated as 240 and 274 in Tables and 2.
- domains VI and VII which generally lie between amino acid residues designated as 470-504 in Tables 1 and 2 . More particularly, as to the human sequence of 2-5A-dependent RNase, domain VI generally lies between amino acid residues designated as 471-491 and domain VII generally lies between amino acid residures designated as 501-504, as reported in Table 1 and FIG. 4. As to the murine sequence of the 2-5A-dependent RNase, domain VI generally lies between amino acids designated as 470-489 and domain VII generally lies between amino acid residues desig ⁇ nated as 499-502, as reported in Table 2 and FIG. 4.
- the limited homology is generally conserved between the murine and human amino acid sequences for 2-5A-dependent RNases and generally lies between a 200 amino acid region. More particularly, for the human sequence, the amino acid region spans amino acid residues designated as 160-349 in Table i and FIGS. 9A and 9B. With respect to the murine sequence, the amino acid region spans amino acid residues designated as 160-348 in Table 2 and FIGS. 9A and 9B.
- the present invention relates to the cloning of murine and human 2-5A-dependent RNases and novel murine and human clones.
- Recombinant and naturally occurring forms of 2-5A-dependent RNase displayed virtually identical 2-5A binding properties and ribonucleas specificities.
- the present invention further contemplates the use of the novel isolated, 2-5A-dependent RNases and encoding sequences therefor, as well as analog and active fragments thereof, for use, for instance, 1.) in gene therapy for human and animal disease including viral disease and cancer, 2.) as geneti markers for human disease due to perhaps cancer o viral infection, 3.) to develop plants and animal resistant to certain viruses, and 4.) as enzymes i connection with research and development, such as fo studying the structure of RNA.
- the encoding sequences of th instant invention may be utilized in ex vivo therapy, i.e., to develop recombinant cells using the encoding sequence of the present invention using techniques known to those versed in this art.
- the encoding sequences of the present invention may be combined with an appropriate promoter to form a recombinant molecule and inserted into a suitable vector for introduction into an animal, plant, or other lower life forms also using techniques known to those skilled in this art.
- suitable methods or means known to those versed in this art may be selected to accomplish the above-stated objectives or other objectives for which the novel 2-5A-dependent RNases and encoding sequences of the present invention are suited.
- the present invention also contemplates novel transgenic plants, as indicated above, which are resistant to viruses such as the picornaviruses.
- the transgenic plants of the present invention include any inserted nucleotide sequence encoding any type of antiviral amino acid sequence, including proteins.
- the antiviral nucleotide sequences introduced into plants in accordance with the present invention are animal antiviral genes, such as those genes which are stimulated in response to interferon productio and/or treatment. These include, for example, thos animal antiviral genes that encode 2-5A-synthetase 2-5A-dependent RNase, and PKR.
- Thes interferon-regulated proteins, 2-5A-synthetase 2-5A-dependent RNase and PKR have recognized antiviral effects i higher animals and are believed to have antivira effects in the transgenic plants of the presen invention.
- PKR is stimulated by dsRNA t phosphorylate translation factor eIF2 whic indirectly inhibits protein synthesis intiation.
- the 2-5A then activates an endoribonucleas entitled 2-5A dependent RNase (also known as RNase or nuclease F) .
- the activated ribonuclease degrade mRNA and rRNA thus inhibiting protein synthesis.
- tha plant viruses are similar to animal viruses i structure, composition and mechanism of replicatio in cells.
- viral so-calle single-stranded RNA may contain secondary structure which could activate PKR and 2-5A synthetase leadin to widespread plant protection against plan viruses. It is believed that co-expression o
- RNA thereby protecting the transgenic plants of th present invention from viruses. Moreover, it i believed that expression of PKR by the transgeni plants of the present invention will inhibit vira protein synthesis leading to inhibition of viru replication and protection of the transgenic plants.
- the present invention is therefore premised in par upon the belief that plant virus RNAs activat
- 2-5A-synthetase and PKR in the transgenic plants o the instant invention leading to immunity agains virus infection. Furthermore, expression of 2-5 synthetase alone or 2-5A-dependent RNase alone or PK alone may protect plants against viruses, perhaps b binding to viral RNA, such as viral replicativ intermediates thereby blocking viral replication.
- expression of only the dsRNA bindin domains of PKR and/or of 2-5A-synthetase ma similarly protect the transgenic plants of th present invention against viral infection.
- the present invention includes, among other things any amino acid sequence, any nucleotide sequence an any transgenic plant which have the ability t accomplish the objectives of the instant invention
- the instant invention includes any amin acid sequence which has antiviral activity and an nucleotide sequence which encodes therefor and thos transgenic plants that express such nucleotid sequences.
- the present inventio includes, for instance: 1.) any animal amino aci sequence which has the ability to inhibit o interfere with viral replication such as those amin acid sequences that have activity similar o identical to PKR activity, 2-5A synthetase activit and/or 2-5A ribonuclease activity, and any nucleotid sequence which encodes for an amino acid sequenc having any such activity; and 2.) any transgeni plant having any animal antiviral nucleotide sequenc which encodes any such amino acid sequence which ha any such antiviral activity.
- FIGS in which is shown illustrative embodiments the present invention from which its novel featur and advantages will be apparent.
- FIG. 1 is the 2-5A system: a ribonuclea pathway which is believed to function in t molecular mechanism of interferon actio 5'-phosphatase, p'tase; 2 , -5 -phosphodiesteras 2'-PDE.
- FIGS. 2A and 2B is a comparison of 2- binding activity of recombinant and natural occurring forms of murine 2-5A-dependent RNase.
- FIG. 2A is a specific affinity of truncat murine 2-5A-dependent RNase for 2-5A.
- UV covale crosslinking of the 32 P-2-5A probe (lanes 1-7) protein is performed after translation reactions wheat germ extract (5 ⁇ l) with murine 2-5A-depende RNase mRNA (from clone ZBl) (lanes 1-3) or withou added RNA (lane 4) or in extract of interfero treated mouse L cells (100 ⁇ g of protein) (lane 5-7) . Reactions are without added competitor (lane 1, 4, and 5) or in the presence of either trime core.
- Lanes and 9 are produced by incubating the wheat ger extract with 35 S-methionine in the absence o presence of 2-5A-dependent RNase mRNA, respectively.
- FIG. 2B are identical chymotrypsin cleavag products and are obtained from recombinant an naturally occurring form of 2-5A-dependent RNase Partial chymotrypsin digests (arrows) are performe on- " truncated 2-5A-dependent RNase (clone ZBl produced in wheat germ extract (“Recombinant”) an murine L cell 2-5A-dependent RNase ("Naturall Occurring”) after crosslinking to the 2-5A probe an purification from gels.
- FIGS. 3A and 3B are clonings of th complete coding sequence for human 2-5A-dependen RNase.
- FIG. 3A is the construction of a huma 2-5A-dependent RNase clone.
- the initial huma 2-5A-dependent RNase cDNA clone, HZB1 is isolate from an adult human kidney cDNA library in ⁇ gtl using radiolabeled murine 2-5A-dependent RNase cDN (clone ZBl) as probe. See Example.
- Radiolabel HZBl DNA is used to isolate a partially overlappi cDNA clone, HZB22, which is fused to HZBl DNA at t Ncol site to form clone ZC1.
- the 5'-region of t coding sequence is obtained from a genomic Sa fragment isolated using a radiolabeled HZB22 D fragment as probe.
- FIG. 3B is a nucleotide sequence a predicted amino acid sequence of human 2-5A-depende RNase with flanking nucleotide sequences. T numbers to the right indicate the positions nucleotides and amino acid residues.
- FIG. 4 is alignment of the predicted amin acid sequences for murine and human forms o 2-5A-dependent RNase. The positions of the repeate P-loop motifs, the cysteine (Cys)-rich regions wit homology to zinc fingers, and the regions of homolog to protein kinase domains VI and VII are indicated Amino acids residues which are important component of the indicated domains are represented in bold typ and are italicized. Identical amino acid residues i murine and human 2-5A-dependent RNase are indicate with colon (:) symbols adjacent therebetween.
- FIGS. 5A and 5B are 2-5A binding propertie and ribonuclease activity of recombinant human 2-5A dependent RNase produced in vitro.
- FIG. 5A is specific affinity of recombinan human 2-5A-dependent RNase for 2-5A.
- Crosslinking o the 2-5A probe (lanes 1-7) to protein is performe after translation reactions in wheat germ extract ( ⁇ l) with human 2-5A-dependent RNase mRNA (lanes 1-3 or without added RNA (lane 4) or in extract of huma interferon ⁇ treated (1000 units per ml for 16 h human HeLa cells (350 ⁇ g of protein) (lanes 5-7) Reactions were without added competitor (lanes 1, 4 and 5) or in the presence of either trimer core (A2'p) 2 A, (100 nM) (lanes 2 and 6) or trimer 2-5A p 3 (A2'p) 2 A (100 nM) (lanes 3 and 7).
- Lane 8 Incubation with 35 S-methionine are shown in lanes 8 to 12.
- Lan 8 is with wheat germ extract and human 2-5A-dependent RNase mRNA.
- Reticulocyte lysate preadsorbed to 2-5A-cellulose is incubated with human 2-5A-dependent RNase mRNA in the absence (lane 9) or presence (lane 10) of cycloheximide, or in the absence of added mRNA (lane 11) .
- Lane 12 shows human 2-5A-dependent RNase which is produced in the nonadsorbed, crude reticulocyte lysate. The positions and relative molecular masses (in kDa) of the marker proteins are indicated.
- FIG. 5B is reticulocyte lysate pretreated to remove endogeous 2-5A-dependent RNase and is incubated in the absence of added mRNA ( ⁇ ) , in the presence of human 2-5A-dependent RNase mRNA without inhibitor ( o , ⁇ ) or in the presence of both 2-5A-dependent RNase mRNA and cycloheximide (50 ⁇ g per ml (•) .
- mRNA ⁇
- human 2-5A-dependent RNase mRNA without inhibitor o , ⁇
- both 2-5A-dependent RNase mRNA and cycloheximide 50 ⁇ g per ml (•) .
- the recombinant 2-5A-dependent RNase or controls
- Radiolabeled substrate RNA was either poly(U) (O, •,B) °r poly(C) (D).
- FIGS. 6A, 6B and 6C show levels of 2-5A-dependent RNase mRNA which are induced by interferon treatment of murine L929 cells even in the presence of cycloheximide.
- FIG. 6A is a northern blot prepared wit poly(A) + RNA (4 ⁇ g per lane) that is isolated fro murine L929 cells treated with murine interferon ( ⁇ ⁇ ) (1000 units per ml) and/or cycloheximide (50 ⁇ per ml) for different durations (indicated) which i probed with radiolabeled murine 2-5A-dependent RNas cDNA. Interferon, IFN; cycloheximide, CHI.
- FIG. 6B shows levels of 2-5A-dependen RNase which are estimated from the autoradiogra shown in panel (a) with a video camera an QuickCapture and Image computer programs.
- FIG. 6C shows levels o glyceraldehyde-3-phosphate dehydrogenase (GAPDH) mRN as determined in the same blot shown in panel (A) .
- GPDH glyceraldehyde-3-phosphate dehydrogenase
- FIGS. 7A and 7B are the truncated recombinant murine 2-5A-dependent RNase, clone ZBl and murine L cell 2-5A-dependent RNase havin identical 2-5A binding activities localized to repeated P-loop motif.
- FIG. 7A shows incubations of truncate 2-5A-dependent RNase, clone ZBl, ("Recombinant” which is produced in wheat germ extract (upper panel or of murine L cell 2-5A-dependent RNase (labele “Naturally Occurring,” lower panel) with the 3 P-2-5 probe, (2.4 nM) , are in the absence of presence o unlabeled 2',5 '-phosphodiester linked oligonucleo tides (as indicated) followed by uv covalen crosslinking. Autoradiograms of the dried SDS/1 polyacrylamide gels are shown. Concentrations of t oligonucleotide competitors are indicated. I inosine.
- FIG. 7B shows a truncated series of muri 2-5A-dependent RNase mutants (ZBl to ZB15) which produced in wheat germ extract which are assayed f 2-5A binding activity by a filter binding metho See Example and Knight et al. 1980) .
- the positio of the P-loop motifs and the lengths of t translation products are indicated.
- Clone Z encodes for amino acids designated as 1-656 in Tab 2 , except for the last 5 amino acid residues whi are Lys, Pro, Leu, Ser, and Gly.
- Clone ZB2 encod for " amino acids designated as 1-619 in Table 2
- Clone ZB3 encodes for amino acids designated as 1-5 in Table 2 .
- Clone ZB5 encodes for amino aci designated as 1-474 in Table 2.
- Clone ZB9 encod for amino acids designated as 1-403 in Table 2
- Clone ZB10 encodes for amino acids designated 1-365 in Table 2
- Clone ZB13 encodes for ami acids designated as 1-294 in Table 2
- Clone ZB encodes for amino acids designated as 1-265 in Tab 2
- Clone ZB15 encodes for amino acids designated 1-218 in Table 2.
- FIGS. 8A and 8B are substitution mutation of the lysine residues in the P-loop motifs o 2-5A-dependent RNase.
- FIG. 8A shows the truncated murin 2-5A-dependent RNase, clone ZBl, and lysine t asparagine substitution mutants of clone ZBl, whic are synthesized in wheat germ extract.
- a unlabeled translation products are covalentl crosslinked to the bromine-substituted, 32 P-labele 2-5A probe, Br-2-5A-[ 32 P]pCp. See Nolan-Sorden e al., 1990.
- FIG. 8B shows the mRNA species which ar translated in the presence of 35 -S-methionine i separate reactions. Autoradiograms of the dried SDS/polyacrylamide gels are shown. The order an positions of the translation products (labelle "RNase") and the relative molecular masses (in kDa of the protein markers are indicated.
- RNase Ribonucleic acid
- FIGS. 9A and 9B are a comparison of th amino acid sequences of RNase E and 2-5A-dependen RNase.
- FIG. 9A shows identical and conservativ matches which are shown between E. coli RNase E an the murine and human forms of 2DR.
- FIG. 9B is a model for the structure an function of 2DR.
- P-loop motifs repeated sequence with homology to P-loops
- Cys ⁇ cysteine-rich region with homology to certain zi fingers
- PK homology to protein kinase domains and VII.
- FIGS. 10A and 10B are a comparison of t amino acid sequences of the ankyrin repeats in t human and murine 2-5A-dependent RNase proteins.
- FIG. 10A shows murine and human forms 2-5A-dependent RNases containing four ankyr repeats. Homology between the ankyrin consens sequence and the murine and human forms 2-5A-dependent RNase are indicated. ⁇ , hydrophob amino acids.
- FIG. 10B is a model showing the relati positions of the four ankyrin repeats in 2-5 .dependent RNase in comparison to the position of t proposed 2-5A binding domain (t) (the repeated P-lo motif) ; Cys ⁇ , the cysteine-rich region; PK, t protein kinase homology region, and t carboxy-terminal region required for RNase activity.
- FIG. 11 shows the role of 2-5A-depende RNase in the anti-viral response of cells interferon treatment.
- Interferon binds to specif cell surface receptors resulting in the generation a signal which activates a set of genes in the ce nucleus.
- the genes for 2-5A synthetase are th activated producing inactive, native 2- synthetase.
- Interferon treatment of the cell al activates the 2-5A-dependent RNase gene (not shown in the FIGure) .
- the interferon-treated cells is infected by a virus.
- the virus produces double stranded RNA (dsRNA) during its replicative cycle.
- the viral dsRNA then activates the 2-5A synthetase resulting in the production of 2-5A.
- the 2-5A then activates the 2-5A-dependent RNase to degrade the viral RNA thus destroying the virus itself.
- dsRNA double stranded RNA
- FIG. 12 depicts a physical map of T: based binary vector p.AM943 which is about 12 Kbp.
- B ⁇ left border
- B j *> right border
- Kan r kanamycin resistance
- .AMT promoter of adenyl methyl transferase gene from Chlorella virus
- 35S promoter for 35S RNA from Cauliflower mosaic virus
- TER RNA termination signal
- FIG. 13 depicts physical maps of portions of certain recombinant plasmid constructs containing cDNAs encoding mammalian antiviral proteins and showing the important DNA elements in between right border and left border of T-DNAs that are transferred to plant genomes.
- FIG. 13A depicts a certain portion of plasmid pAM943:PK68;
- FIG. 13B depicts a certain portion of plasmid pAM943:muPK68;
- FIG. 13C depicts a certain portion of plasmid pAM943:Synthetase;
- FIG. 13D depicts a certain portion of plasmid pAM943:2-5A-dep.
- RNase sense
- FIG. 13D/a depicts certain portion of plasmid pAM943:2-5A-dep.
- RNase an FIG. 13E depicts pAM822:2-5A dep.
- RNase antisense
- B L left border
- Hygro r hygromyci resistance
- AMT promoter of adenyl methy transferase gene from Chlorella virus
- 35S promote for 35S RNA from Cauliflower mosaic virus
- PKR cDN to human PKR
- uPKR cDNA to a lysine (amino acid 296) to arginine mutant form of PKR
- Synthetase cDN to a low molecular weight form of huma 2-5A-synthetase
- 2-5Adep RNase, cDNA to huma 2-5A-dependent RNase
- TER RNA termination signal.
- FIG. 14 shows a physical map of Ti base binary vector pAM822 which is about 14.6 Kbp.
- B L left border
- Hygro r hygromyci resistance
- Tet r tetracycline resistance
- 35S promoter for 35S RNA fro Cauliflower mosaic virus
- TER RNA terminatio signal
- Ovi V origin of DNA replication.
- FIG. 15 shows expression of huma 2-5A-synthetase cDNA intransgenic tobacco plants a determined by measuring mRNA levels in a Norther blot.
- Construct C pAM943:Synthetase
- Total RNA was prepared from th leaves of control (labeled "C") and transgenic plant using RNASTAT-60 (Tel-Test B. , Inc.). Thirty ⁇ g o RNA was treated with glyoxal and separated in a 1.5 agarose gel.
- FIG. 16 shows expression of mutant and wil type forms of human PKR cDNA in transgenic tobacc plants as determined by measuring mRNA levels in Northern blot.
- Constructs A pAM943:PK68
- pAM943: uPK68 encoding wild type and mutant (lysin at position 296 to arginine) forms of PKR respectively, were introduced into the plants.
- Tota RNA was prepared from the leaves of control (labele "C") and transgenic plants using RNASTAT-60 (Tel-Tes B. , Inc.). Thirty ⁇ g of RNA was treated with glyoxa and separated in a 1.5% agarose gel.
- FIG. 17 shows a presence of 2-5A-dependen RNase cDNA in transgenic plants as determined on Southern blot.
- Genomic DNA was isolated from leave of transgenic plants containing construct D/ (pAM943:2-5A-dep. Nase, antisense) using CTA (cetyltrimethylammonium bromide) following the metho of Rogers and Bendich (1988, Plant Molecular Biolog Manual, A6, pp. 1-10, Kluwar Academic Pulbisher Dordrecht) .
- CTA cetyltrimethylammonium bromide
- Ten ⁇ g of genomic DNA was digested wit Hindlll for 5 h at 37'C and fractionated in a 1 agarose gel followed by transfer to Magnagraph (nylo transfer membrane. Micron Separations, Inc.) using capillary transfer method.
- the cDNA fo 2-5A-dependent RNase (from plasmid pZC5) was labele by random priming with [ ⁇ - 32 P]dCTP (3,000 Ci/mmole using a Prime-a-gene kit from (Promega) according t the protocol supplied by the company.
- the labele 2-5A-dependent RNase cDNA (Specific activity of 1.0 10 9" c.p.m. per ⁇ g DNA) was washed and a autoradiogram was made from the dried membrane. Th sizes (in kilobases) and the positions of the DN markers are indicated. The band indicated a "2-5A-dep. RNase cDNA" (see arrow) was absent i Southern blots of control plants (data not shown) .
- FIG. 18 depicts a coding sequence for hum p68 kinase mRNA (PKR) .
- FIG. 19 depicts a translation product the complete coding sequence for human p68 kina mRNA (PKR) of FIG. 18.
- FIG. 20 depicts a coding sequence for hum 2-5A synthetase cDNA.
- FIG. 21 depicts a translation product the coding sequence for human 2-5A-synthetase of FI 20. Detailed Description
- 2-5A-dependent RNase is very low abundance (one five-hundred-thousandth of the tot •protein in mouse liver, Silverman, R.H. et al., Biol. Chem.. 263:7336-7341 (1988)), its cloni requires the development of a sensitive screeni method.
- Murine L929 cells are selected as the sour of mRNA due to high basal levels of 2-5A-depende RNase.
- a protocol to enhance 2-5A-dependent RNa mRNA levels is developed based on the observati that optimal induction of 2-5A-dependent RNase obtained by treating cells with both interferon a cycloheximide, then with medium alone.
- the cDNA is transcribed a translated in cell-free systems. See Example.
- 2- ⁇ binding activity is then determined by covalent crosslinking the 2-5A probe to the protein with light, for example, Nolan-Sorden, N.L. et al., Ana Biochem.. 184:298-304 (1990).
- the recombinant 74 k protein produced in a wheat germ extract sho specific affinity for the 2-5A probe. See FIG. 2 lanes 1 to 3.
- a core derivative of 2-5A lacki 5'-phosphoryl groups, (A2 p) 2 A, fails to interfe with binding of the protein to the 2-5A probe where trimer 205A, p3(A2 , p) 2 , completely prevents pro binding. See FIG. 2A, lanes 2 and 3, respectivel There is no detectable 2-5A binding proteins in t wheat germ extract as shown in the incubation witho added RNA, FIG. 2A, lane 4.
- a composite DN containing genomic and cDNA is constructed. See FIG 3A.
- the initial cDNA portion of the huma 2-5A-dependent RNase clone (HZBl) is obtained b screening a human kidney cDNA library wit radiolabeled murine 2-5A-dependent RNase cDNA.
- Se Example. A genomic clone, containing the 5'-part o the coding sequence, is isolated with radiolabele human 2-5A-dependent RNase cDNA.
- the nucleotide an predicted amino acid sequences of huma 2-5A-dependent RNase are determined, FIG. 3B resulting an open reading frame encoding a protein o 83,539 Da.
- FIG. 4 A comparison is made between the predicte amino acid sequences of the human and murine forms o 2-5A-dependent RNase in order to identify an evaluate the conserved regions of the proteins. Se FIG. 4.
- the murine cDNA, clone ZBl contains abou 88% of the coding sequence for 2-5A-dependent RNas to which an additional twenty-eight 3'-codons ar added from a murine genomic clone. Alignment of th murine and human forms of 2-5A-dependent RNas indicates about 65% identity between the overlappin regions. See FIG. 4.
- the 2-5A binding properties of th recombinant and naturally occurring forms of huma 2-5A-dependent RNase are compared by uv covalen crosslinking to the 2-5A probe.
- the recombinan human 2-5A-dependent RNase produces in wheat ger extract shows specific affinity for 2-5A. See FIG 5A, lanes 1 to 3. Radiolabeling of the cloned huma 2-5A-dependent RNase with the 2-5A probe is no prevented by (A2 , p) 2 A. See FIG. 5A, lanes 1 and 2 In contrast, addition of trimer 2-5A, p 3 (A2 , p) A effectively competes with the 2-5A probe for bindin to the recombinant 2-5A-dependent RNase.
- FIG. 5A lanes 9 and 12 show t 35 S-translation products produced in t 2-5A-cellulose-pretreated and untreated lysate respectively.
- Ribonuclease assays with recombina 2-5A-dependent RNase are performed after immobilizi and purifying the translation product on t activating affinity matrix, 2-5A-cellulose. It w previously shown that murine L cell 2-5A-depende RNase bound to 2-5A-cellulose, resulting ribonuclease activity against poly(U) but n poly(C) . See Silverman, R.H., .Anal. Biochem. 144:450-460 (1985). Furthermore, by washin 2-5A-dependent RNase:2-5A-cellulose prior to addin the substrate the level of general non-2-5A-dependent RNase, is greatly reduced. Se Silverman, R.H. , .Anal. Biochem..
- the murine and human 2-5A-dependent RNas mRNAs are determined from northern blots to be 5.7 k and 5.0 kb in length, respectively. See FIG. 6A.
- the 2-5A-dependent RNase coding sequences therefore, comprise only about 40% the nucleotide sequence contained in the mRNAs.
- the 2-5A binding functions of th recombinant and naturally occurring forms of murin 2-5A-dependent RNase are characterized by covalen crosslinking to the 2-5A probe in the presence o unlabeled 2-5A or 2-5A analogues as competitors.
- Se FIG. 7A Interestingly, although the about 74 kD truncated 2-5A-dependent RNase is missing about 84 amino acids from its carboxy-terminus, see FIG. 4, i nonetheless possesses a 2-5A binding activit indistinguishable from that of naturally occurrin 2-5A-dependent RNase. See FIG. 7A. Trime 2-5A[p 3 (A2'p) 2 A] , at about 20 nM effectively prevent the 2-5A probe from binding to either protein.
- FIG. 7B Expression of clon ZBll, encoding amino acid residues 1 to 342, result in- a loss of only about 26% of the 2-5A bindin activity as compared to clone ZBl (amino acids 1 t 656). See FIG. 7B. Clones intermediate in lengt between ZBl and ZBll all result in significant level of 2-5A binding activity. In contrast, protei produced from ZB13 (amino acids 1 to 294) results i only about 38.3% of the 2-5A binding activity o clone ZBl, suggesting that a region important for th 2-5A binding function is affected.
- clon ZB14 produced a protein encoding amino acids 1 to 26 which is nearly inactive in the 2-5A binding assa (only 1.9% of th activity of clone ZBl)
- the significant decrease in 2-5 binding activity observed with ZB14 occurs with t deletion of one of two P-loop motifs; nucleoti binding domains in many proteins.
- FIGS. 4 a 7B See also Saraste, M. et al., TIBS. 14:430-4 (1990) .
- Deletion of both P-loop motifs in clone ZB results in protein (amino acids 1 to 218) which completely lacking in 2-5A binding activity.
- S FIG. 7B Deletion of both P-loop motifs in clone ZB results in protein (amino acids 1 to 218) which completely lacking in 2-5A binding activity.
- FIG. 8B Similar levels of proteins are synthesized from the different mRNA species as shown in separate reactions containing 35 S-methionine. See FIG. 8B.
- the three mutant forms of 2-5A-dependent RNase shows reduced binding to the 2-5A probe. See FIG. 8A, lanes 2 to 4.
- Clone ZBl(Lys 240 -)Asn) FIG. 8A, lane 2, expresses a mutant 2-5A-dependent RNase with a substantially reduced affinity for 2-5A; about 48.4% of the activity of clone ZBl as determined by phosphorimager analysis .(Molecular Dynamics) of the dried gel.
- the full-length huma 2-5A-dependent RNase which is produced i reticulocyte lysate, had the same apparent molecula weight as did naturally occurring 2-5A-dependen RNase. See FIG. 5A. However, the actual molecula mass of human 2-5A-dependent RNase is determined fro the predicted amino acid sequence, FIG. 3B, to be about 83,539 Da.
- interferon i believed to regulate the 2-5A pathway by elevatin levels of both 2-5A synthetases, Hovanessian, A.G. e al.. Nature, 268:537-539 (1977), and 2-5A-dependen RNase, Jacobsen, H. et al.. Virology. 125:496-50 (1983a). See. FIGS. 1, 6 and 11.
- the cloning of 2-5A-dependent RNase reveal several features of the protein.
- the 2-5A bindin domain is of particular interest because it is th ability of 2-5A-dependent RNase to be activated b 2-5A that sets it apart from other nucleases.
- the identified region contains repeated P-loop motif, one from residues 229 to 24 and another from residues 253 to 275. See FIG. 4 an Table 2.
- P-loop motif amino acid 253-275
- the homology with P-loops is believed to b highly conserved between the human and murine form of 2-5A-dependent RNase; thus underscoring the belie of the importance of this region for 2-5A bindin activity. See FIG. 4.
- the similarity to P-loop consists of the tripeptides, glycine-lysine threonine, preceded by glycine-rich sequences.
- the unusual feature of 2-5A-dependen RNase is that the P-loop motif is repeated and are i the same orientation.
- Adenylyl cyclase from Bacillu anthracis also contains a duplicated P-loop motif, however, the two sequences are in opposit orientation and are overlapping. See Xia, Z. an Storm, D.R. , J. Biol. Chem.. 265:6517-6520 (1990).
- dimer 2-5A neither binds 2-5A-dependent RNas efficiently nor does it activate 2-5A-dependen RNase, FIG. 7A; Kerr, I.M. and Brown, R.E. , Prod Natl. Acad. Sci. U.S.A.. 75:265-260 (1978) an Knight, M. et al., Nature, 288:189-192 (1980) perhaps because it is too short to span the tw P-loop motifs.
- the residual 2-5 binding activity observed in the point mutants ZBl(Lys 240 ->Asn) and ZBl(Lys 274 -)Asn) , and the ver low affinity of the double mutant ZBl(Lys 240 ' 274 ->Asn) for 2-5A, could indicate tha the two P-loop motifs are parts of separate 2-5 binding domains.
- a consensus zinc finger domain reviewed i Evans, R.M. and Hollenberg, S.M. , Cell. 52:1- (1988) , consisting of six cysteine residues with th structure CX 4 CX 3 CX ⁇ 7 CX 3 CX 3 C (amino acid residue 401-436 in Table 2 ) is identified in the murine for of 2-5A-dependent RNase. See FIG. 4. The homologou region in the human form of 2-5A-depenent RNase i CX 11 CX 25 CX 3 CX ⁇ C (amino acid numbers 395 to 444 i Table 1 ) .
- the cysteine-rich region i 2-5A-dependent RNase could be involved in binding t the RNA substrate.
- the cysteine-ri domain in 2-5A-dependent RNase could media formation of 2-5A-dependent RNase dimers.
- the homol with RNase E is relatively conserved between human and murine forms of 2-5A-dependent RNase spans a region of about 200 amino acid residu Within these regions there are 24 and 32% identi plus conservative matches, with some gaps, betw RNase E and the human and murine forms 2-5A-dependent RNase, respectively.
- FIG. The me gene which encodes RNase E and the alte mRNA stability (ams) gene, Ono, M. and Kumano, M., Mol. Biol.. 129:343-357 (1979), map to the s genetic locus. See Mudd E.A. et al., M Microbiol.. 4:2127-2135 (1990); Babitzke, P. and Kushner, S.R. , Proc. Natl. Acad. Sci. U.S.A.. 88:1-5
- RNase E is required for both efficient mRNA turnover and rRNA processing in E. coli. See Mudd E.A. et al., Mol. Microbiol.. 4:2127-2135 (1990) and Babitzke, P. and Kushner, S.R. , Proc. Natl. Acad. Sci. U.S.A.. 88:1-5 (1991).
- the cleavage specificities of 2-5A-dependent RNase and RNase E are similar in that 2-5A-dependent RNase cleaves mainly after UU or UA, Wreschner, D.H. et al.. Nature.
- Endoribonucleases play a controlling role in RNA metabolism by catalyzing the rate-limiting steps in RNA decay. See Brawerman, G. , Cell, 57:9-10 (1989) .
- 2-5A-dependent RNase is a uniquely regulated endoribonuclease which mediates effects of interferon against picornaviruses. It functions by binding 2-5A and subsequently degrades both viral and cellular RNA. See Wreschner, D.H. et al., Nucleic Acids Res.. 9:1571-1581 (1981b).
- the 2-5A system may be involved in the antiproliferative effects of interferon and in the fundamental control of RNA stability.
- the source of mRNA for preparing the cDNA library is murine L929 cells grown in EMEM
- Synthesis of the first strand of cDNA is done by using reverse transcriptase as described (Superscript; BRL) except that 5-methyl-dCTP is substituted for dCTP and an Xhol-oligo-dT adapter-primer (Stratagene) is used.
- Synthesis of the second strand of cDNA and ligation of EcoRI linker was as described (Stratagene) .
- the cDNA is digested with EcoRI and Xhol and unidirectionally cloned into predigested ⁇ ZAPII vector (Stratagene) .
- the library is packaged by using Giagpack Gold extract and titered on PLK-F bacteria.
- the cDNA library is screened directly without prior amplification at a density of about 25,000 phage per 150 mm plate. Phage are grown for 3.5 hours at about 42°C until plaques are visible. Nitrocellulose filters saturated in IPTG (10 mM) and then dried, are overlaid on the plates and growth was continued for an additional 4 to 6 hours at 37°C. The filters are processed by a modification of the ethods of Singh, H. et al.. Cell. 52:415-423 (1988) and Singh, H. et al., BioTechniques. 7:252-261 (1989) .
- Filters are washed in ice-cold binding buffer (about 20 mM Tris-HCl, about pH 7.5, about 20 mM magnesium acetate, about 50 mM potassium chloride, about 1 mM EDTA, about 50 mM ⁇ -mercaptoethanol, about 0.1 mM PMSF, about 5% glycerol) containing about 6 M guanidine-HCl for about 20 min.
- the solution containing the filters is then diluted two-fold with binding buffer and washing on ice is continued for about an additional 5 minutes; serial two-fold dilutions were continued until the guanidine concentration was about 187 mM.
- the filters are then washed twice with binding buffer, and incubated with binding buffer containing about 5% nonfat milk for one hour at about room temperature.
- the filters are then washed twice with binding buffer and incubated in binding buffer (supplemented with about 0.25% nonfat dry milk and about 0.02% sodium azide) containing p(A2'p) 2 (br 8 A2'p) 2 A3'-[32P]Cp (the "2-5A probe"), Nolan-Sorden, N.L. et al.. Anal. Biochem.. 184:298-304 (1990), at about 2 X 10 5 counts per minute per ml (about 3,000 Ci per mmole) at about 4°C with shaking for about 24 hours.
- Murine L929 cells are treated with about 1000 units per ml interferon ( ⁇ + ⁇ ) with or without about 50 ⁇ g per ml of cycloheximide and the total RNA is then isolated as described. See Chomczynski, P. and Sacchi, N., Anal. Biochem.. 162:156-159 (1987).
- Poly(A) + RNA is prepared by oligo(dT)-cellulose chromatography, as described in Sambrook, J. et al.. Cold Spring Harbor Laboratory Press (1989) , and is separated on glyoxal agarose gels and transferred to Nytran membranes.
- RNA is immobilized on the membrane by uv crosslinking (Stratalinker, Stratagene) .
- the murine 2-5A-dependent RNase cDNA is 32 P-labeled by random priming and then hybridized to the filter [about 50% formamide, about 10% dextran sulphate, Denhardt's solution about 1% SDS, 6X SSPE, Sambrook, J. et al. , Cold Spring Harbor Laboratory Press (1989) , about 250 ⁇ g per ml salmon sperm DNA] at about 42°C.
- the Human 2-5A-dependent RNase cDNA clone, HZBl is isolated from an adult human kidney cDNA library in ⁇ gtlO with radiolabeled (random primed) murine 2-5A-dependent RNase cDNA (clone ZBl) as probe, Sambrook, J. et al.. Cold Spring Harbor Laboratory Press (1989) .
- Clone HBZ22 is isolated using radiolabeled HZBl DNA as probe.
- the genomic human 2-5A-dependent RNase clone is isolated from a human placenta cosmid library in vector pVE15 (Stratagene) with a radiolabeled fragment of HZB22 DNA as probe.
- the murine genomic 2-5A-dependent RNase clone is isolated from a mouse 129SV genomic library in vector ⁇ FIXII (Stratagene) with a radiolabeled fragment of 2-5A-BP cDNA (clone ZBl) as probe. Subcloning of DNA is in Bluescript vectors (Stratagene) .
- RNA polymerases Transcription of plasmids with phage RNA polymerases is in the presence of mGppppG as described (Promega) except that reaction mixtures are supplemented with 15% dimethyl sulfoxide and incubations are at about 37°C for about 90 minutes.
- RNA is purified through Sephadex G50 spun-columns and ethanol precipitated prior to translation. Protein synthesis was performed, as described (Promega) , at about 30°C for about one hour in micrococcal nuclease-pretreated rabbit reticulocyte lysate or in an extract of wheat germ at about room temperature for about one hour and then at about 40°C for about 12 hours.
- Translation reactions contain about 50 ⁇ M zinc sulfate.
- Endogenous 2-5A-dependent RNase in the reticulocyte lysated is removed by adsorption to about 30 ⁇ M of p 2 (A2'p) 3 A covalently attached to cellulose (2-5A-cellulose) , prepared as described in Wells, J.A. et al., J. Biol. Chem.. 259:1363-1370 (1984) and Silverman, R.H. and Krause, D. , I.R.L. Press. Oxford. England, pp. 149-193 (1987) , for about one hour on ice as described. See Silverman, R.H. , .Anal. Biochem.. 144:450-460 (1985).
- the 2-5A-dependent RNase:2-5A-cellulose complex is removed by twice centrifuging at about 400 x g for about 5 minutes at about 2°C. The supernatant completely lacking in measurable levels of 2-5A-dependent RNase. See FIG. 5.
- the set of nested 3'-deletions of the truncated murine 2-5A-dependent RNase cDNA, ZBl is generated with exonuclease III/Sl nuclease digestion followed by filling-in with Klenow DNA Polymerase using the "Erase-A-Base" system (Promega) .
- the synthesis of the 2-5A probe, p(A2'p) 2 (br 8 A2'p) A[32P]Cp, and its crosslinking to 2-!-5A-dependent RNase is performed exactly as described. See Nolan-Sorden, N.L. et al., Anal. Biochem.. 184:298-304 (1990). Briefly, the 2-5A probe, about 0.7 to 2.5 nM at 3,0009 ci/mmole, is incubated for about one hour on ice with cell extract prepared as described, Silverman, R.H. and Krause, D. , I.R.L. Press. Oxford. England, pp.
- Covalent crosslinking is done under a uv lamp (308 nm) for one hour on ice and the proteins are separated on SDS/10% polyacrylamide gels. Filter assays for 2-5A binding activity using the 2-5A probe for about one hour on ice, as described in Knight, M. et al.. Nature, 288:189-192 (1980).
- Protease digestions are performed o gel-purified proteins in a gel, as described b Cleveland, D.W. et al., J. Biol. Chem.. 252:1102-110 (1977).
- the ribonuclease assay with 2-5A-cellulos is performed, as described by Silverman, R.H. , Anal. Biochem.. 144:450-460 (1985). Briefly, lysates ar adsorbed to about 30 ⁇ M of 2-5A-cellulose on ice fo about two hours. The matrix is then washed thre times by centrifuging and resuspending in buffer A. See Silverman, R.H. , Anal. Biochem.. 144:450-46 (1985).
- the matrix is then incubated wit poly(U)-[ 32 P]Cp or poly(C)-[ 32 P]Cp (both at about 1 ⁇ M in nucleotide equivalents) at about 30°C and th levels of acid-precipitable radioactive RNA ar determined by filtration on glass-fiber filters.
- the Sanger dideoxy sequencing method i used to determine the DNA sequences (Sequenase, United States Biomedical) .
- the lysines in the truncated murin 2-5A-dependent RNase, clone ZBl, at positions 240 an 274 are mutated, individually and together, t asparagine residues. Mutants ZBl(Lys 274 ->Asn) an the double mutant, ZBl(Lys 240,274 -)Asn) , are obtaine with mutant oligonucleotides after subcloning ZB cDNA into pALTER-1 as described (Promega) .
- Mutant ZBl(Lys 240 -)Asn) is obtained after polymerase chain reaction amplification of a segment of ZBl with an upstream primer containing a unique Hindi site attached to the mutant sequence and a second primer downstream of a unique Bglll site.
- the Hindi- and BGlII-digested polymerase chain reaction product and similarly-digested clone ZBl are then ligated.
- the specific mutations are: for codon 240, AAA->AAC and for codon 274, AAG->AAC. Mutants are confirmed by DNA sequencing. EXAMPLE II
- Seeds of tobacco (Nicotiana tabacum cv. Wisconsin) and Ti based binary vectors pAM943 and pAM822 were obtained from Dr. Amit Mitra, Department of Plant Pathology, University of Kansas, Lincoln, Kansas.
- the plant tissue culture medium Murashige and Skoog's ready mix (MS media) was purchased from Sigma Chemical Company, St. Louis, Missouri.
- the human cDNAs for PKR, the lysine • ⁇ arginine mutant PKR, and 2-5A synthetase were obtained from Dr. B.R.G. Williams, Department of Cancer Biology, The Cleveland Clinic Foundation. See, for example, Meurs, E. et al.: Cell. 62:379-390 (1990); Chong, K.L. et al.: EMBO J.. 11:1553-1562 (1992); Rysieki, G. et al.: J. Interferon Res.. 9:649-657 (1989); Benech, P. et al.: EMBO J.. 4:2249-2256 (1985); and Saunders, M.E.
- the expression vector pAM943 is used to obtain Argobacterium-mediated transfer of T DNA containing the cDNAs and kanamycin resistance marker gene.
- the physical map of the plasmid vector pAM943 shows its elements. See FIG. 12.
- the plasmid pAM943 contains a dual promoter consisting of the adenyl methyl transferase (AMT) gene promoter of Chlorella virus and the wild type 35S promoter of Cauliflower mosaic virus.
- the vector also contains the gene for kanamycin resistance to select the transformed plants.
- the cDNAs are subcloned in pAM943 and amplified in E. coli strains K802 or MM294 using tetracycline resistance as the selectable marker.
- the Argobacterium cells are transformed with the recombinant pAM943 plasmids and selected by growth in medium containing about 5 ⁇ g/ml of tetracycline. about 10 ⁇ g/ml of kanamycin and about 25 ⁇ g/ml of streptomycin.
- PK68 a lysine •* arginine mutant PKR (muPk ⁇ ; the mutant PKR protein binds to dsRNA but has no kinase activity and will thus function as a control)
- a low molecular weight form of 2-5A-synthetase (synthetase)
- the plasmids pKS(+)PKR, pKS(+)muPKR, and pKS(+)synthetase are digested first with Xbal and than with Clal restriction endonucleases, the cDNA fragments are purified from low melting point agarose gels and subcloned in sense orientation at Xbal and Clal sites of pAM943.
- the recombinant plasmids e.g., construct A, pAM943:PK68, construct B, pAM943:muPK68, and contruct C, pAM943:synthetase, which correspond to the constructs depicted in FIG. 13A-C, respectively, are used to transform Argobacterium tumefaciens LBA4404.
- the resultant bacteria identified as AG68, AGmu68 and AGsyn, respectively, are used for tobacco leaf disc transformations.
- the plasmid pKS(+)2C5 DNA is digested with Hindlll enzyme and subcloned in the Hindlll site of pAM943 in both orientations, see FIG. 13, and the recombinant plasmids, construct D, pAM943:2-5A-dep.
- RNase antisense both of which correspond to constructs D and D/a, respectively, in FIG. 13D and D/a, are used to transform Argobacterium to obtain the bacteria called AG2DR sense and AG2DR antisense, respectively.
- the competent Argobacterium cells are prepared and transformation follows the method of, for * example. An, G. et al.: Plant Molecular Biology Manual. AD:1-19 (1988). The presence of recombinant plasmids in the transformed Argobacterium cells is confirmed by preparing plasmid DNA and by performing PCR using specific complementary oligonucleotides and by observing restriction enzyme digests.
- the cDNA used fo 2-5A-dependent RNase is in plasmid pZC5 referenced i Zhou et al. Cell 72, 753-765 (1994), the human for of the cDNA.
- the sequence is also disclosed herein.
- the plasmid pAM822 contains a second selectabl marker gene, the hygromycin resistance gene, permitting the construction of plants containing bot 2-5A-synthetase and 2-5A-dependent RNase cDNAs. Insertion of pAM822:2-5Adep.
- RNase Fig. 13E
- containing 2-5A-dependent RNase cDNA int kana ycin-resistant, transgenic tobacco leaf disc containing 2-5A-synthetase cDNA is thus performed.
- Tobacco plants are grown aseptically i Murashige and. Skoog's medium, known as MS medium, containing about 3% sucrose (MSO medium) and abou 0.8% agar in plastic boxes (Phytatray) at about 28° under cycles consisting of about 16 hr of light an about 8 hr of dark in a growth chamber. Leave bigger than about 2" long are cut into about 2 to 3 cm 2 pieces under the MSO medium and 6-8 leaf piece are placed in a 6 cm Petri dish containing about 2 m of MSO medium and holes are made in the leaf piece with a sterile pointed forcep.
- MS medium containing about 3% sucrose (MSO medium) and abou 0.8% agar in plastic boxes (Phytatray) at about 28° under cycles consisting of about 16 hr of light an about 8 hr of dark in a growth chamber.
- Leave bigger than about 2" long are cut into about 2 to 3 cm 2 pieces under the MSO medium and 6-8 leaf piece are placed in a 6 cm
- Leaf pieces are washed extensively with MSO medium and transferred to solid agar for selection in shoot regeneration medium [MSO; about 0.5 mg/1 BAP (benzylaminopurine) ; about 200 ⁇ g/ml kanamycin; about 200 ⁇ g/ml carbenicillin; and about 100 ⁇ g/ml of cefotaxine] , under diffuse light at about 28 ⁇ C in the growth chamber.
- shoot regeneration medium [MSO; about 0.5 mg/1 BAP (benzylaminopurine) ; about 200 ⁇ g/ml kanamycin; about 200 ⁇ g/ml carbenicillin; and about 100 ⁇ g/ml of cefotaxine] , under diffuse light at about 28 ⁇ C in the growth chamber.
- shoot regeneration medium [MSO; about 0.5 mg/1 BAP (benzylaminopurine) ; about 200 ⁇ g/ml kanamycin; about 200 ⁇ g/ml carbenicillin; and about 100 ⁇ g/ml of cefotaxine
- the transgenic plants expressing 2-5A synthetase are substantially transformed to introduce the cDNA for 2-5A-dependent RNase (with pAM9 3:2-5Adep.RNase sense, construct D; FIG. 13D) .
- the vector pAM822 FIG. 14
- the vector pAM822 FIG. 14
- the vector pAM822 FIG. 14
- the vector pAM822 FIG. 14
- Tissue culture and regeneration of plants are done as described above.
- Transgenic plants are grown to produce flowers and seeds to demonstrate the transfer of the antiviral genes or nucleotide sequences to subsequent generations.
- specific plasmid constructs are described herein, the present invention is intended to include any plant vector including those with
- FIG. 16 shows expression of mutant and wild type forms of human PKR cDNA in transgenic tobacco plants as determined by measuring mRNA levels in a Northern blot.
- FIG. 17 depicts presence of 2-5A-dependent RNase cDNA in transgenic tobacco plants as determined on a Southern blot.
- FIG. 13A Plasmid pAM943:muPK68
- Antisense 1 + N.T. N.T.
- a Tobacco plants contain construct D, pAM943:2-5Adep. RNa (sense) .
- 2-5A binding assays are performed by the filt binding method of Knight, M. et al. Nature (288) :189-1 (1980) with modifications.
- a 32 P-labeled and bromi substituted 2-5A analog, p(A2'p) 2 (br 8 A2'p) 2 A3'- 32 p]C about 15,000 counts per min per assay, at about 3,000 per mmole, Nolan-Sorden, N.L. , et al. Anal. Biochem.
- leaves are collected from transgenic plants containing 2-5A-dependent RNase cDNA and they are homogenized in NP40 lysis buffer, see Silverman, R.H. and Krause, D. (1987) In, Clemens, M.J., Morris, A.G., and Gearing, A.J.H., (eds.), Lymphokines and Interferons - A Practical Approach. I.R.I. , Press, Oxford, pp.
- Extracts are clarified by centrifugation at about 10,000 x g for about 10 min.
- Supernatants of the extracts, about 100 ⁇ g of protein per assay, are separated by SDS/10% polyacrylamide gel electrophoresis, followed by transfer of the proteins to Immobilon-P membrane filters (Millipore Corp., Bedford, MA). The filter is then incubated with about 4 X 10 5 c.p.m.
- Antiviral activity of the plants are determined by rubbing celite powder coated with Tobacco mosaic virus (ATCC) and Tobacco Etch virus (from Dr. Amit Mitra, Iowa) . The plants are monitored for symptoms of viral infection on leaves from control and transgenic plants and are documented in photographs.
- ATCC Tobacco mosaic virus
- Dr. Amit Mitra, Iowa Tobacco Etch virus
- the plasmids described and the transformed Argobacterium strains can be used to transform any other plants into virus-resistant plants.
- Exemplary of plants that may be transformed in accordance with the present invention include vegetable plants like corn, potato, carrot, lettuce, cabbage, broccoli, cauliflower, bean, squash, pumpkin, pepper, onion, tomato, pea, beet, celery, cucumber, turnip and radish plants, fruit plants like banana, apple, pear, plum , apricot, peach, nectarine, cherry, key lime, orange, lemon, lime, grapefruit, grape, berry, and melon plants, grain plants like wheat, barley, rice, oat and rye plants, grass, flowers, trees, shrubs and weeds such as laboratory weeds like Arabidopsis.
- the present invention includes any plant into which any nucleotide sequence encoding an amino acid having antiviral activity has been introduced to form transgenic plants having immunity or resistance against viral infection.
- PKR nucleotide sequence utilized to construct plasmids pKS(+)PKR and pKS(+)muPKR is depicted in
- FIG. 18 To determine the ability of a plant translation apparatus to synthesize PKR protein, capped PKR mRNA is produced from linearized pKS(+)PKR by in vitro transcription. The RNA is then translated in wheat germ extract (obtained from
- the cDNAs encoding PKR and muPKR are excised from plasmids pKS(+)PKR and pKS(+)muPKR by digesting with Kpnl and Xbal. The resulting DNA fragments containing the entire coding sequences for PKR and muPKR are purified from a low melting point agarose gel. To generate cDNAs containing at the 5' end Xbal and at the 3' end Clal sites, the PKR cDNA and muPKR cDNA are then digested with Clal and purified.
- the resulting digested PKR cDNA and muPKR cDNA are then force cloned into Xbal and Clal digested pAM943 by DNA ligation.
- the resulting plasmids FIG. 13, constructs A and B, are used to transform Argobacterium tumefaciens strain LBA4404 (Clonetech, Plao Alto, CA) .
- Recombinant plasmids are prepared from transformed Argobacterium tumefaciens bacteria by standard methods and the presence of PKR and muPKR cDNA is confirmed by PCR analysis and restriction enzyme digests of the isolated plasmids. Construction of pAM943:Synthetase Iconstruct C)
- the plasmid ptac-15 containing the human cDNA illustrated in FIG. 20 for a small form of 2-5A-synthetase (producing a 1.8 kb mRNA) (obtained from Dr. B.R.G. Williams, Cleveland Clinic, Cleveland, Ohio) is prepared by standard methods and is digested with BamHI and EcoRI.
- the synthetase cDNA is purified from a low melting point agarose gel by standard methods and is then subcloned into plasmid pKS(+) (Strategene, La Jolla, CA) in BamHI and EcoRI sites.
- Recombinant plasmids are prepared from transformed Argobacterium tumefaciens bacteria by standard methods and the presence of 2-5A-synthetase cDNA is confirmed by PCR analysis and by restriction enzyme digests of the isolated plasmids.
- the plasmid pKS(+)ZC5 encoding a complete coding sequence for human 2-5A-dependent RNase is digested with Hindlll.
- 2-5A-dependent RNase is purified in a low melting point agarose gel and is then subcloned in Hindlll digested pAM943 in both sense (forward) and antisense
- Transformed Argobacterium are determined to contain the 2-5A-dependent RNase cDNA by restriction enzyme digests and by PCR analysis. Construction of pAM822:2-5Adep.RNase antisense fconstruct Ei
- PCR Polymerase chain reactions
- PCR primers 2-5A-dependent RNase to generate Hindlll and BamHI sites on the two ends of the cDNA and to reduce 5' and 3' untranslated sequences.
- the PCR primers used are:
- H2DR-4 5'-GATACTCGAGAAGCTTGCATCCTCATCAGCACCCAGGGCTGG -3'.
- the PCR product (about 2.25 kbp) is purified on a low melting point agarose gel and is then digested with
- this seed contains construct D, shown in Fig. 13, which is pAM943:2-5Adep.RNase ••this seed contains construct C, shown in Fig. 13, which is pAM943 -Synthetase T.AB B 1 Hwna ⁇ -1 2-5A-depedent RNase
- SEQ ID NO:l «, SEQ ID NO:2:, SEQ ID NO:3: and SEQ ID N0:
- GCT CTC ATG GAC GCT GCT GAA AAA GGA CAC 540
- Val Glu Val Leu Lys lie Leu Leu Asp Glu 190
- ATT ACG CAT CTG CTG CTG GAC CAT GGG GCT 690 lie Thr His Leu Leu Leu Asp His Gly Ala 230
- AAG AAA GCT GCT CAC 1500 lie Leu lie Asp Ser Lys Lys Ala Ala His 500 CTG GCA GAT TTT GAT AAG AGC ATC AAG TGG 1530
- Lys Trp Thr Thr Lys lie Asn Glu Cys Val 640
- Met Lys Leu Lys lie Gly Asp Pro Ser Leu 690
- ATC TAT GTC TAC ACA AAA CTA CAG AAC ACA 2130 lie Tyr Val Tyr Thr Lys Leu Gin Asn Thr 710
- SEQ ID NO:1 represents the DNA encoding sequence for the human 2-5A-dependent RNase protein.
- SEQ ID NO:2 represents the amino acid sequence encoded by the DNA sequence designated SEQ ID N0:1:.
- SEQ ID NO:3: represents the DNA sequence, represented by SEQ ID NO:l:, having the alternative codon number 95, CCT.
- SEQ ID NO:4: represents the amino acid sequence encoded by SEQ ID NO:3: , having the alternative amino acid number 95, proline.
- SEQ ID NO:5 represents the DNA sequence encoding Murine 2-5A-dependent RNase (partial).
- SEQ ID NO:6 represents the amino acid sequence encoded by SEQ ID N0:5:.
- MOLECULE TYPE DNA (genomic)
- GGG GCT GAT GTC AAT GTG AGG GGA GAA AGA GGG AAG ACT CCC CTG ATC 83 Gly Ala Asp Val Asn Val Arg Gly Glu Arg Gly Lys Thr Pro Leu lie 230 235 240
- GCC AAA GAA GAT TTT CAC CCT CCT GCT GAA GAC TGG .AAG CCT CAG AGC 1123 Ala Lys Glu Asp Phe His Pro Pro Ala Glu Asp Trp Lys Pro Gin Ser 325 _ - 330 335 340
- AAG CAT AAA AAG ATG AAA TTA AAA ATT GGA GAC CCT TCC CTG TAT TTT 2179 Lys His Lys Lys Met Lys Leu Lys He Gly Asp Pro Ser Leu Tyr Phe 680 685 690
- MOLECULE TYPE DNA (genomic)
- GGG GCT GAT GTC AAT GTG AGG GGA GAA AGA GGG AAG ACT CCC CTG ATC 83 Gly Ala Asp Val Asn Val Arg Gly Glu Arg Gly Lys Thr Pro Leu lie 230 235 240
- GCC AAA GAA GAT TTT CAC CCT CCT GCT GAA GAC TGG AAG CCT CAG AGC 11 Ala Lys Glu Asp Phe His Pro Pro Ala Glu Asp Trp Lys Pro Gin Ser 325 330 335 340
- AAG CAT AAA AAG ATG AAA TTA AAA ATT GGA GAC CCT TCC CTG TAT TTT 2179 Lys His Lys Lys Met Lys Leu Lys lie Gly .Asp Pro Ser Leu Tyr Phe 680 685 690
- MOLECULE TYPE DNA (genomic)
- ATC CAG GGA GAT GTG AAA CTG CTC GAG ATT CTC CTC TCT TGT GGT GCA 51 lie Gin Gly Asp Val Lys Leu Leu Glu lie Leu Leu Ser Cys Gly Ala 105 110 115
- CAA CCA CAA AAC ATC TTA ATA GAT TCC AAG AAA GCT GTC CGG CTG GCA 166 Gln Pro Gin Asn lie Leu lie Asp Ser Lys Lys Ala Val Arg Leu Ala 485 490 495 500
- MOLECULE TYPE protein
- Glu Lys Gly His Leu-Glu Val Leu Arg lie Leu Leu Asn Asp Met Lys 180 185 190
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Abstract
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Priority Applications (3)
Application Number | Priority Date | Filing Date | Title |
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EP95911802A EP0753992A4 (en) | 1994-02-18 | 1995-02-16 | Antiviral transgenic plants, vectors, cells and methods |
BR9507425A BR9507425A (en) | 1994-02-18 | 1995-02-16 | Transgenic plant transgenic tobacco plant plant transformation vector plant cell differentiated tobacco plant bacterial cell tobacco plant Process for genetically producing transformed plants building isolated nucleotide sequence and amino acid sequence |
AU19234/95A AU706185B2 (en) | 1993-03-08 | 1995-02-16 | Antiviral transgenic plants, vectors, cells and methods |
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US19897394A | 1994-02-18 | 1994-02-18 | |
US08/198,973 | 1994-02-18 |
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PCT/US1995/002058 WO1995022245A1 (en) | 1993-03-08 | 1995-02-16 | Antiviral transgenic plants, vectors, cells and methods |
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EP (1) | EP0753992A4 (en) |
BR (1) | BR9507425A (en) |
CA (1) | CA2183461A1 (en) |
WO (1) | WO1995022245A1 (en) |
Cited By (6)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
WO1996040948A2 (en) * | 1995-06-07 | 1996-12-19 | Research Corporation Technologies, Inc. | RESISTANCE TO VIRUSES AND VIROIDS IN TRANSGENIC PLANT AND ANIMAL HOSTS EXPRESSING dsRNA-BINDING PROTEIN |
US6326466B1 (en) * | 1996-07-30 | 2001-12-04 | The United States Of America As Represented By The Secretary Of The Department Of Health And Human Services | Double-stranded RNA dependent protein kinase derived peptides to promote proliferation of cells and tissues in a controlled manner |
WO2003023011A2 (en) * | 2001-09-12 | 2003-03-20 | Isis Pharmaceuticals, Inc. | Antisense modulation of ribonuclease l expression |
US8951768B2 (en) | 2005-05-04 | 2015-02-10 | Kineta Two, Llc | Mutations in OAS1 genes |
US9090947B2 (en) | 2003-10-23 | 2015-07-28 | Kineta Two, Llc | Detection of mutations in a gene associated with resistance to viral infection, OAS1 |
CN114591978A (en) * | 2021-09-30 | 2022-06-07 | 湖南大学 | Application of OsFLR14 gene in improving resistance of rice to weeds |
Family Cites Families (4)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
EP0217102B1 (en) * | 1985-08-28 | 1992-01-08 | Yeda Research And Development Company, Ltd. | Interferon-induced (2'-5') oligo a synthetase gene, mrna, cdna and enzymes having (2'-5') oligo a synthetase activity |
WO1993019187A1 (en) * | 1992-03-18 | 1993-09-30 | Kemira Bio Holding B.V. | Transgenic plants displaying multiple virus resistance and a process for their production |
KR100260483B1 (en) * | 1992-04-17 | 2000-07-01 | 마나배 게이사꾸 | Plants resistant against plural viruses and method |
AU6403694A (en) * | 1993-03-08 | 1994-09-26 | Cleveland Clinic Foundation, The | Animal 2-5a-dependent rnases and encoding sequences therefor |
-
1995
- 1995-02-16 EP EP95911802A patent/EP0753992A4/en not_active Withdrawn
- 1995-02-16 CA CA002183461A patent/CA2183461A1/en not_active Abandoned
- 1995-02-16 BR BR9507425A patent/BR9507425A/en not_active Application Discontinuation
- 1995-02-16 WO PCT/US1995/002058 patent/WO1995022245A1/en not_active Application Discontinuation
Non-Patent Citations (16)
Cited By (8)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
WO1996040948A2 (en) * | 1995-06-07 | 1996-12-19 | Research Corporation Technologies, Inc. | RESISTANCE TO VIRUSES AND VIROIDS IN TRANSGENIC PLANT AND ANIMAL HOSTS EXPRESSING dsRNA-BINDING PROTEIN |
WO1996040948A3 (en) * | 1995-06-07 | 1997-04-03 | Res Corp Technologies Inc | Resistance to viruses and viroids in transgenic plant and animal hosts expressing dsrna-binding protein |
US6326466B1 (en) * | 1996-07-30 | 2001-12-04 | The United States Of America As Represented By The Secretary Of The Department Of Health And Human Services | Double-stranded RNA dependent protein kinase derived peptides to promote proliferation of cells and tissues in a controlled manner |
WO2003023011A2 (en) * | 2001-09-12 | 2003-03-20 | Isis Pharmaceuticals, Inc. | Antisense modulation of ribonuclease l expression |
WO2003023011A3 (en) * | 2001-09-12 | 2003-11-27 | Isis Pharmaceuticals Inc | Antisense modulation of ribonuclease l expression |
US9090947B2 (en) | 2003-10-23 | 2015-07-28 | Kineta Two, Llc | Detection of mutations in a gene associated with resistance to viral infection, OAS1 |
US8951768B2 (en) | 2005-05-04 | 2015-02-10 | Kineta Two, Llc | Mutations in OAS1 genes |
CN114591978A (en) * | 2021-09-30 | 2022-06-07 | 湖南大学 | Application of OsFLR14 gene in improving resistance of rice to weeds |
Also Published As
Publication number | Publication date |
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EP0753992A4 (en) | 1998-02-04 |
BR9507425A (en) | 1997-09-16 |
EP0753992A1 (en) | 1997-01-22 |
CA2183461A1 (en) | 1995-08-24 |
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