Ex Parte Matringe et alDownload PDFPatent Trial and Appeal BoardFeb 21, 201711078038 (P.T.A.B. Feb. 21, 2017) Copy Citation United States Patent and Trademark Office UNITED STATES DEPARTMENT OF COMMERCE United States Patent and Trademark Office Address: COMMISSIONER FOR PATENTS P.O.Box 1450 Alexandria, Virginia 22313-1450 www.uspto.gov APPLICATION NO. FILING DATE FIRST NAMED INVENTOR ATTORNEY DOCKET NO. CONFIRMATION NO. 11/078,038 03/11/2005 Michel Matringe 037759.00014 1668 4372 7590 02/23. ARENT FOX LLP 1717 K Street, NW WASHINGTON, DC 20006-5344 EXAMINER KRUSE, DAVID H ART UNIT PAPER NUMBER 1663 NOTIFICATION DATE DELIVERY MODE 02/23/2017 ELECTRONIC Please find below and/or attached an Office communication concerning this application or proceeding. The time period for reply, if any, is set in the attached communication. Notice of the Office communication was sent electronically on above-indicated "Notification Date" to the following e-mail address(es): patentdocket @ arentfox. com PTOL-90A (Rev. 04/07) UNITED STATES PATENT AND TRADEMARK OFFICE BEFORE THE PATENT TRIAL AND APPEAL BOARD Ex parte MICHEL MATRINGE, PASCAL RIPPERT, MANUEL DUBALD, and RENAUD DUMAS1 Appeal 2015-008267 Application 11/078,038 Technology Center 1600 Before MELANIE L. McCOLLUM, RICHARD J. SMITH, and DAVID COTTA, Administrative Patent Judges. McCOLLUM, Administrative Patent Judge. DECISION ON APPEAL This is an appeal under 35 U.S.C. § 134 involving claims to a method for cultivating a transformed plant. The Examiner has rejected the claims as obvious. We have jurisdiction under 35 U.S.C. § 6(b). We affirm. STATEMENT OF THE CASE Claims 15, 16, 24, and 26—32 are pending and on appeal (Br. 2). Claim 16 is representative and reads as follows: 16. A method for increasing the tolerance of a plant to an inhibitor of a /7-hydroxyphenylpyruvate dioxygenase, the method comprising: 1 Appellants identify the real party in interest as Bayer S.A.S. (Br. 2). Appeal 2015-008267 Application 11/078,038 a) applying an herbicidal composition comprising an inhibitor of /7-hydroxyphenylpyruvate dioxygenase to a plant transformed with: (1) a first gene that is functional in a plant, wherein the first gene comprises a nucleotide sequence that encodes a yeast prephenate dehydrogenase, and (2) a second gene that is functional in a plant, wherein the second gene comprises a nucleotide sequence that encodes a p-hydroxyphenyl- pyruvate dioxygenase, and wherein the plant overexpresses the prephenate dehydrogenase and the /7-hydroxyphenylpyruvate dioxygenase, thereby increasing the tolerance of said plant to an inhibitor of a p-hydroxyphenylpyruvate dioxygenase, wherein said plant is tolerant to an amount of said inhibitor that is toxic to or decreases the growth of plants transformed with said second gene alone, and b) cultivating the plant. Claims 15, 16, 24, and 26—32 stand rejected under 35 U.S.C. § 103(a) as obvious over Sailland2 in view of Valentin,3 Matringe,4 UniProtKB Accession No. P20049, Meazza,5 Berg,6 and Rippert7 (Ans. 2). Relying on Meazza, the Examiner finds that “HPPD [p-hydroxy- phenylpyruvate dioxygenase] catalyzes the conversion of p-hydroxyphenyl- pyruvate (HPP) to homogentisate (a key precursor of at least alpha 2 Sailland et al., US 6,268,549 Bl, July 31, 2001. 3 Valentin et al., US 7,112,717 B2, Sept. 26, 2006. 4 Matringe et al., WO 02/46441 A2, June 13, 2002. 5 Giovanni Meazza et al., The Inhibitory Activity of Natural Products on Plantp-Hydroxyphenylpyruvate Dioxygenase, 59 Phytochemistry 281—88 (2002). 6 Jeremy M. Berg et al., Biochemistry § 8.5 (5th ed. 2002). 7 Pascal Rippert & Michel Matringe, Molecular and Biochemical Characterization of an Arabidovsis thaliana Arogenate Dehydrogenase with Two Highly Similar and Active Protein Domains, 48 Plant Molecular Biology 361-68 (2002). 2 Appeal 2015-008267 Application 11/078,038 tocopherol)” and that “HPPD inhibitors are competitive inhibitors (competing with HPP)” (id. at 5). Relying on Berg, the Examiner also finds: a hallmark of competitive inhibition (at least as compared to noncompetitive inhibition) is that because substrate (here, HPP) and inhibitor (here, DKN, for example) are both competing for the catalytic site of the enzyme (here, HPPD), competitive inhibition may be overcome by increasing the substrate concentration so that the substrate may “outcompete” the inhibitor for the catalytic site of the enzyme. (Id.) In addition, relying on Rippert, the Examiner finds that “it was known that PDH [prephenate dehydrogenase] catalyzes the conversion of prephenate to HPP” (id.). The Examiner relies on Sailland for teaching “the overexpression of HPPD within a plant to increase the tolerance of that plant to HPPD inhibitors and ‘weeding plants’ with an herbicide application to transformed plants pre-sowing, pre-emergence and post-emergence” (id. at 6). The Examiner acknowledges that Sailland does “not teach PDH” (id.). The Examiner relies on Valentin for teaching “cultivating a plant transformed with a[n] Erwinia herbicola PDH and an Arabidopsis HPPD nucleotide sequence to increase tocopherol and tocotrienol levels within the plant” (id.). The Examiner acknowledges that Valentin does “not teach a yeast PDH gene” (id. at 7). The Examiner relies on Matringe for teaching “yeast PDH (corresponding to EC 1.3.1.13) (. . . see also UniProtKB Accession Number P20049 which teaches a yeast PDH corresponding to EC 1.3.1.13)” and “the expression of yeast PDH or bacterial PDH (including Erwinia herbicola PDH . . .) within plants to complement herbicide inhibited plant 3 Appeal 2015-008267 Application 11/078,038 arogenate/prephenate dehydrogenase” (id. ). The Examiner finds that Matringe “teach[es], therefore, that at least bacterial and yeast PDHs have synonymous functionalities such that either may be used to at least complement plant arogenate/prephenate dehydrogenase” (id.). The Examiner concludes: At the time the present invention was made, it would have been obvious to a person of ordinary skill in the art to overexpress plant HPPD within a plant (as did Sailland et al.) and additionally overexpress yeast PDH within that plant so as to overcome HPPD competitive inhibitor herbicide compositions (or at least render the plant more tolerant to such herbicide compositions) because it would amount to no more than the combination of two well-recognized solutions for circumventing competitive inhibition (increase both substrate and enzyme concentrations to outcompete inhibitor) with known methods (overexpression of plant HPPD (Sailland et al....) and yeast PDH (Matringe et al.) within a plant) to arrive at the claimed subject matter with a reasonable expectation of success in view of Valentin et al. (teaching the expression of HPPD and PDH within a plant) and Sailland et al. (teaching the overexpression of HPPD within a plant). (Id.) FINDINGS OF FACT 1. Sailland “relates to the use of a gene coding for HPPD in a process for the transformation of plants” (Sailland, col. 1,11. 64—65). 2. Sailland discloses “plant cells,. . . especially of crops, transformed according to one of the processes described above and comprising in their genome an efficacious quantity of a[] gene expressing hydroxyphenylpyruvate dioxygenase (HPPD)” (id. at col. 2,11. 59-64). 4 Appeal 2015-008267 Application 11/078,038 3. Sailland also discloses that it “has been observed that transformed plants of this type have a significant tolerance to certain novel herbicides such as the isoxazoles . . . and especially isoxaflutole, a selective maize herbicide, the diketonitriles . . . , the triketones ... in particular sulcotrione” {id. at col. 2,1. 64, to col. 3,1. 9). 4. In addition, Sailland discloses “a method of weeding plants, especially crops, with the aid of a[n] herbicide of this type, characterized in that this herbicide is applied to plants transformed according to the invention, both pre-sowing, pre-emergence and post-emergence of the crop” {id. at col. 3,11. 10-14). 5. Meazza discloses that “HPPD catalyzes the conversion of /7-hydroxyphenyl pyruvate (4-HPP) to homogentisate (HGA). . . , which is a key precursor of a-tocopherol and plastoquinone” (Meazza 281). 6. Meazza also discloses: “HPPD inhibitors have introduced new classes of herbicides based on the triketone backbone which apparently mimics a reaction intermediate. These compounds are time-dependent (tight-binding) inhibitors of this enzyme. Sulcotrione . . . and isoxaflutole ... are commercial products belonging to two of such classes.” {Id.) 7. In addition, Meazza discloses that, “[sjince most synthetic triketone herbicides targeting HPPD are competitive tight-binding inhibitors, their binding to the catalytic site is for all practical purposes irreversible” {id. at 282). 8. Berg discloses: “A competitive inhibitor diminishes the rate of catalysis by reducing the proportion of enzyme molecules bound to a substrate. At any given inhibitor concentration, competitive inhibition can 5 Appeal 2015-008267 Application 11/078,038 be relieved by increasing the substrate concentration. Under these conditions, the substrate ‘outcompetes’ the inhibitor for the active site.” (Berg § 8.5.) 9. Rippert Figure 1 is set forth below: Ft 3~plwsspM*e EPBP symft&m 4 -EWipfep ..... fSa 9 $ rm !:?:S *•••••: r. j;™0 i-iSj AMf \ # SiijC- C $:s« «M8fM!5#WS Rippert Figure 1 depicts the biosynthesis pathway leading to tyrosine (Rippert 362). 6 Appeal 2015-008267 Application 11/078,038 10. Rippert discloses: Two alternatives exist in nature for the conversion of prephenate into tyrosine . . . (Figure 1). In the majority of green bacteria, some other micro-organisms, algae and the majority of plant species analysed so far, L-tyrosine is synthesized via the arogenate pathway.... Prephenate, in this case, is transaminated into arogenate by a specific transaminase .... Arogenate is then transformed into L-tyrosine by arogenate dehydrogenase [ADH], . . . Alternatively, in other organisms such as Escherichia coli and yeast, prephenate is first transformed into p-hydroxyphenyl- pyruvate by NADH+-dependent prephenate dehydrogenase . . . and then transaminated to L-tyrosine. {Id. at 361.) 11. Valentin “relates to genes and polypeptides associated with the tocopherol biosynthesis pathway, namely those encoding homogentisate prenyl transferase activity, and uses thereof’ (Valentin, col. 1,11. 10-12). 12. As depicted in its Figure 1, Valentin teaches: [In higher plants, the] plant tocopherol pathway can be divided into four parts: 1) synthesis of homogentisic acid (HGA) . . . ; 2) synthesis of phytylpyrophosphate . . . ; 3) joining of HGA and phytylpyrophosphate via a homogentisate prenyl transferase followed by a subsequent cyclization; and 4) S-adenosyl methionine dependent methylation of an aromatic ring, which affects the relative abundance of each of the tocopherol species. {Id. at col. 2,11. 53-67.) 13. To synthesize HGA, Valentin teaches: In at least some bacteria the synthesis of homogentisic acid is reported to occur via the conversion of chorismate to prephenate and then to p-hydroxyphenylpyruvate via a bifimctional prephenate dehydrogenase. Examples of bifimctional bacterial prephenate dehydrogenase enzymes include the proteins encoded by the tyrA genes of Erwinia herbicola and Escherichia coli. The tyrA gene product catalyzes the production of 7 Appeal 2015-008267 Application 11/078,038 prephenate from chorismate, as well as the subsequent dehydrogenation of prephenate to form p-hydroxyphenyl- pyruvate (p-HPP), the immediate precursor to homogentisic acid. p-HPP is then converted to homogentisic acid by hydroxyphenylpyruvate dioxygenase (HPPD). In contrast, plants are believed to lack prephenate dehydrogenase activity, and it is generally believed that the synthesis of homogentisic acid from chorismate occurs via the synthesis and conversion of the intermediate arogenate. Since pathways involved in homogentisic acid synthesis are also responsible for tyrosine formation, any alterations in these pathways can also result in the alteration in tyrosine synthesis and the synthesis of other aromatic amino acids. {Id. at col. 3,11. 32—52.) 14. Valentin discloses: In an embodiment of the present invention, exogenous genetic material encoding a homogentisate prenyl transferase enzyme or fragment thereof is introduced into a plant with one or more additional genes. In one embodiment, preferred combinations of genes include a nucleic acid molecule of the present invention and one or more of the following genes: tyrA . . . , prephenate dehydrogenase . . . , HPPD .... {Id. at col. 23,11. 32-45.) 15. In particular, Valentin exemplifies expression of a homogentisate prenyl transferase (HPT) as a single gene and in combination with HPPD and tyrA in soy, specifically “the Arabidopsis p-hydroxyphenyl- pyruvate dioxygenase (HPPD4 and the bifimctional prephenate dehydrogenase from Erwinia herbicola (tyrAEhT {id. at col. 57,11. 35—61). Valentin states that, “[wjhile expression of ATPT2 or slrl736[, which are species of HPT,] increased total tocopherol and tocotrienol levels in soy moderately, the impact of HPT expression in the context of a multi gene 8 Appeal 2015-008267 Application 11/078,038 vector was much more pronounced” and that “[t]hese data suggest that combination of an HPT with tyrA, and HPPD can substantially enhance tocopherol biosynthesis in soy” {id. at col. 58,11. 25—35, & col. 3,11. 8—9). 16. Matringe “relates to transgenic plants tolerant to a herbicidal compound having as a target an enzyme involved in one of the metabolic steps of conversion of prephenate to L-tyrosine, characterized in that they contain a gene encoding a prephenate dehydrogenase enzyme and express said enzyme in their tissue” (Matringe,8 col. 10,11. 20—26). 17. Matringe also discloses that “the gene encoding the prephenate dehydrogenase enzyme expressed in the tolerant plants ... is a yeast gene” {id. at col. 10,11. 49-51). ANALYSIS Sailland discloses transformed plant cells “comprising in their genome an efficacious quantity of a[] gene expressing hydroxyphenylpyruvate dioxygenase (HPPD)” (Finding of Fact (FF) 2). Sailland also discloses “a method of weeding plants, especially crops, with the aid of a[n] herbicide [that is an HPPD inhibitor], characterized in that this herbicide is applied to plants transformed according to the invention” (FF 3, 4, & 6). The issue raised in this appeal is whether it would have been obvious to additionally include a gene comprising a nucleotide sequence that encodes yeast PDH. Meazza discloses that “most synthetic triketone herbicides targeting HPPD are competitive tight-binding inhibitors” (FF 7). Berg discloses that 8 The point citations to Matringe are to its US counterpart, US 7,279,302 B2, which was used by the Examiner as an English-language equivalent (Ans. 2). 9 Appeal 2015-008267 Application 11/078,038 “competitive inhibition can be relieved by increasing the substrate concentration” (FF 8). The substrate for HPPD is p-hydroxyphenyl pyruvate (FF 5). Rippert discloses that PDH is an enzyme that can be used to form p-hydroxyphenyl pyruvate from prephenate (FF 9—10). In addition, Valentin discloses a plant transformed with both HPPD and tyrA (a bifimctional PDH) to enhance tocopherol biosynthesis (FF 15 & 13). Furthermore, Matringe specifically discloses transformation with a yeast PDH (FF 16—17). In view of these disclosures, we conclude that the Examiner has set forth a prima facie case that it would have been obvious to additionally include a gene comprising a nucleotide sequence that encodes yeast PDH in order to increase the amount of the /7-hydroxyphenyl pyruvate substrate (Ans. 7). Appellants argue, however, “that the combination of seven cited references . . . amounts to an impermissible hindsight reconstruction of the methods of the claims” (Br. 10). We are not persuaded. The Examiner explains how each of the references is being used to support the conclusion of obviousness (Ans. 5—8). We conclude that Appellants have not adequately explained why the Examiner’s position was a hindsight reconstruction. In particular, we do not find that the fact that seven references were applied demonstrates in and of itself that hindsight was used. Appellants also contend that “Matringe et al. does not support a reasonable expectation of success because Matringe et al. does not refer to the same mechanism for providing herbicide tolerance against inhibitors” and that “[tjhere is nothing in either Sailland et al. or Matringe et al. [that] 10 Appeal 2015-008267 Application 11/078,038 would lead persons skilled in the art to express both HPPD and PDH in a plant to increase tolerance of plants to HPPD inhibitor type herbicides” (Br. 12). Appellants additionally argue: The knowledge of different solutions for overcoming the effects of herbicides does not lead persons skilled in the art to combine the solutions in one plant, especially where the solutions relate to different herbicides and herbicide targets. Thus, the cited references do not present a reasonable expectation of success of increasing tolerance of plants to HPPD inhibitor type herbicides. (Id. at 13.) We are not persuaded. Sailland discloses a plant transformed with a gene that encodes HPPD (FF 2). Matringe discloses a plant transformed with a gene that encodes yeast PDH (FF 16—17). We agree that the Examiner has not shown that Sailland and Matringe alone suggest a plant that is transformed with both of these genes. Instead, it is the combination of all of the applied references, as discussed herein, that leads to this conclusion. In addition, Appellants argue that “it is not clear from Valentin et al. whether the increase in tocopherol content is due to expression of HPPD and PDH alone or the combination of EPSPS, HPPD and PDH” (Br. 11). Appellants also argue that “Valentin et al. discloses expression of both HPPD and tyrA in soybean to increase tocopherol content of the seeds, but, due to the unclear teachings of the reference, discussed above, does not provide a reasonable expectation to the skilled person that this would succeed” (id. at 12). Appellants additionally argue that “Valentin et al. does not disclose or suggest applying herbicides to the plants or increasing tolerance of plants to HPPD inhibitor type herbicides” and therefore “does not provide persons skilled in the art with a reasonable expectation of 11 Appeal 2015-008267 Application 11/078,038 success for increasing tolerance of plants to HPPD inhibitor type herbicides” {id. at 13). We are not persuaded. Valentin discloses “exogenous genetic material encoding a homogentisate prenyl transferase enzyme or fragment thereof is introduced into a plant with one or more additional genes,” such as HPPD, PDH, and tyrA (FF 14). In particular, Valentin discloses expression of a homogentisate prenyl transferase (HPT) in combination with both HPPD and tyrA, which is a bifimctional PDH (FF 15 & 13). Valentin also discloses that, “[w]hile expression of [HPT] increased total tocopherol and tocotrienol levels in soy moderately, the impact of HPT expression in the context of a multi gene vector was much more pronounced” and that the “data suggest that combination of an HPT with tyrA, and HPPD can substantially enhance tocopherol biosynthesis in soy” (FF 15). It is undisputed that the “constructs used in Example 6 of Valentin et al. all express an EPSPS enzyme in addition to the HPPD and PDH” (Br. 11). However, Appellants have not shown, and it is not clear to us, how this is excluded by the claims. In any event, we agree with the Examiner that the teachings of Valentin provide a reasonable expectation for success in forming a plant that has been transformed with genes encoding both HPPD and PDH, as well as suggest that one of ordinary skill in the art would have had reason to add both genes to a plant. We recognize that Valentin relates to enhancing tocopherol biosynthesis rather than increasing tolerance of plants to HPPD inhibitor type herbicides (FF 15). However, given the teaching in Valentin of adding both genes to increase tocopherol, we are not persuaded that one of ordinary skill in the art would not have thought based 12 Appeal 2015-008267 Application 11/078,038 on the applied references that both genes would be helpful to increasing the tolerance of plants to HPPD inhibitor type herbicides. Appellants also argue that Meazza teaches “that HPPD inhibitors are competitive tight-binding inhibitors, making their binding to the catalytic site for all practical purposes irreversible” (Br. 13). In addition, Appellants argue that Berg “teaches that for competitive inhibitors, the inhibition can be overcome by increasing the substrate concentration,” but “specifies that this teaching mostly works with reversible inhibitors, not with irreversible inhibitors” (id.). Thus, Appellants argue that “the skilled person would have serious doubts from the combined teachings of Berg et al. and Meazza et al. that the known irreversible competitive inhibition of HPPD inhibitors could reasonably be overcome by increasing the HPP substrate concentration in the plants” (id. at 14). We are not persuaded. We note Appellants’ argument that Berg “specifies” that overcoming inhibition by increasing substrate concentration “mostly works with reversible inhibitors, not with irreversible inhibitors” (id. at 13). However, Appellants have not identified, and we did not find, where this is specified. Thus, we conclude that Appellants have not adequately demonstrated that “the skilled person would have serious doubts from the combined teachings of Berg et al. and Meazza et al. that the known irreversible competitive inhibition of HPPD inhibitors could reasonably be overcome by increasing the HPP substrate concentration in the plants” (id. at 14). In addition, Appellants argue “that the motivation put forward by the Examiner for combining the references is merely a conclusory statement, 13 Appeal 2015-008267 Application 11/078,038 and is not a sufficient basis for combining the cited references in the manner set out in the Office Action” (id. at 15). We are not persuaded. The Examiner provides fact-based reasoning to support the conclusion of obviousness (Ans. 5—8). We conclude that Appellants have not adequately explained why the Examiner’s reasoning is not supported by the applied references. Appellants also argue that “[tjhere is nothing in any of the cited references, alone or in combination that would lead a person skilled in the art to recognize that transformed plants overexpressing PDH and HPPD exhibit greater tolerance to HPPD inhibitors” (Br. 15). In particular, Appellants argue that “there is nothing in the cited references that would lead the skilled person to conclude that overexpressing both PDH and HPPD in a plant would increase the tolerance of the plant to HPPD inhibitors” and “there is no disclosure or suggestion that PDH could be associated with tolerance to HPPD inhibitors” (id.). Therefore, Appellants argue that it was “surprising and unexpected that plants overexpressing both PDH and an HPPD would be tolerant to an amount of HPPD inhibitor that is toxic to or decreases the growth of plants transformed with HPPD alone” (id.). We are not persuaded. PDH catalyzes the conversion of prephenate to p-hydroxyphenyl pyruvate, the substrate of HPPD (FF 5 & 9). “[Competitive inhibition can be relieved by increasing the substrate concentration” (FF 8). In addition, “most synthetic triketone herbicides targeting HPPD are competitive tight- binding inhibitors” (FF 7). Furthermore, Valentin teaches introducing a gene encoding PDH, as well as HPPD, to increase the amount of tocopherol 14 Appeal 2015-008267 Application 11/078,038 (FF 14—15). Thus, we do not agree with Appellants that “there is no disclosure or suggestion that PDH could be associated with tolerance to HPPD inhibitors” (Br. 15). In addition, Sailland teaches that overexpression of HPPD increases tolerance of the plant to HPPD inhibitors (FF 1—3 & 6). Thus, we agree with the Examiner that it would have been obvious to include both genes in the same plant with a reasonable expectation of improved results (Ans. 7—8). CONCLUSION The evidence supports the Examiner’s conclusion that the applied references suggest the method of claim 16. Claims 15, 24, and 26—32 have not been argued separately and therefore fall with claim 16. 37 C.F.R. § 41.37(c)(l)(iv). TIME PERIOD FOR RESPONSE No time period for taking any subsequent action in connection with this appeal may be extended under 37 C.F.R. § 1.136(a). AFFIRMED 15 Copy with citationCopy as parenthetical citation