PTAB

IPR2019-00581

Associated British Foods v. Cornell Research Foundation Inc

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Petition
petition

1. Case Identification

2. Patent Overview

  • Title: Overexpression of Phytase Genes in Yeast Systems
  • Brief Description: The ’150 patent discloses methods for producing phytase, an enzyme used in animal feed. The methods involve expressing a heterologous polynucleotide from a non-yeast organism (encoding either PhyA or AppA phytase) in a yeast host cell and then isolating the enzyme, which is claimed to have increased thermostability compared to the same enzyme expressed in a non-yeast host.

3. Grounds for Unpatentability

Ground 1: Obviousness over Kretz and Cheng - Claims 1-4, 6-9, 21, 28-34, and 39

  • Prior Art Relied Upon: Kretz (Patent 5,876,997) and Cheng (Patent 5,985,605).
  • Core Argument for this Ground:
    • Prior Art Mapping: Petitioner argued that Kretz disclosed all essential steps of the claimed method: providing a heterologous polynucleotide encoding an E. coli phytase (an obvious variant of the claimed AppA phytase), expressing this phytase in yeast host cells, and isolating the resulting protein. Kretz also taught that its E. coli phytase was innately thermostable. While Kretz did not specify a yeast species, Cheng taught methods for expressing bacterial phytases in well-characterized, industrially suitable yeasts like Pichia to achieve high yields and efficiency. Petitioner asserted the claimed "increased thermostability" is an inherent and expected result of expressing a bacterial protein in a yeast host, which can perform glycosylation, a modification that enhances stability.
    • Motivation to Combine: A person of ordinary skill in the art (POSITA) would combine Kretz's disclosure of a highly thermostable E. coli phytase with Cheng's efficient, high-yield production methods in an industrial yeast host like Pichia. The motivation was economic: to increase the volume and efficiency of enzyme production while reducing costs, creating a commercially viable phytase for use as an animal feed additive.
    • Expectation of Success: A POSITA would have a reasonable expectation of success because Kretz already taught expressing the E. coli phytase in yeast, and Cheng provided established methods for expressing similar bacterial phytases in Pichia, a "well characterized" host.

Ground 2: Obviousness over Greiner, Dassa, and Cheng - Claims 1-4, 6-9, 21, 28-34, and 39

  • Prior Art Relied Upon: Greiner (a 1993 journal article), Dassa (a 1990 journal article), and Cheng (Patent 5,985,605).
  • Core Argument for this Ground:
    • Prior Art Mapping: This ground replaced Kretz with prior art that explicitly disclosed the claimed AppA phytase. Dassa discovered and taught the complete polynucleotide sequence for the E. coli appA gene. Greiner subsequently confirmed that the protein encoded by Dassa's appA gene was, in fact, an AppA phytase with high specificity and stability at various temperatures and pH levels. Cheng, as in Ground 1, provided the enabling disclosure for expressing bacterial phytases in an efficient yeast system like Pichia.
    • Motivation to Combine: A POSITA would be motivated to express the specific, advantageously stable AppA phytase disclosed by Greiner and Dassa using the industrially viable and high-yield yeast expression system taught by Cheng. Greiner's teaching that AppA phytase was an attractive option for animal feed would have driven a POSITA to seek the most efficient production method available, which Cheng provided.
    • Expectation of Success: The expectation of success was high. The exact gene sequence and its beneficial properties were known from Dassa and Greiner, and Cheng taught that its methods were suitable for expressing phytases from various bacteria in yeast.

Ground 3: Obviousness over Greiner, Dassa, Romanos, and Van Gorcom - Claims 1-4, 6-9, and 28-34

  • Prior Art Relied Upon: Greiner (a 1993 journal article), Dassa (a 1990 journal article), Romanos (a 1995 journal article), and Van Gorcom (Patent 5,436,156).

  • Core Argument for this Ground:

    • Prior Art Mapping: Similar to Ground 2, Greiner and Dassa disclosed the specific AppA phytase and its encoding polynucleotide. This combination replaced Cheng with Romanos and Van Gorcom to establish the motivation for yeast expression. Romanos identified Pichia as a "mainstream expression host" known to produce "extremely high yields." Van Gorcom taught general, industrial-scale methods for producing phytases (including from bacteria) in various microbial hosts, including yeasts, and methods for isolating the final product.
    • Motivation to Combine: A POSITA would be motivated to take the desirable AppA phytase from Greiner and Dassa and produce it using an economically viable, high-yield system. Romanos provided the motivation to select Pichia as the host due to its superior yields, and Van Gorcom provided the established industrial methods for expressing and purifying phytase in such hosts. The goal was economical, large-scale production.
    • Expectation of Success: A POSITA would have expected success because Van Gorcom taught that phytase genes have a high degree of homology across species, suggesting a bacterial phytase like AppA would be expressible using methods for other phytases. Further, Romanos established Pichia as a reliable host for expressing bacterial enzymes.

  • Additional Grounds: Petitioner asserted that claims 1-4, 6-9, 21, and 39 were also obvious based on the combinations in Grounds 1, 2, and 3 further in view of Olsen (a 1991 journal article). Olsen was argued to provide an explicit teaching and additional motivation for expressing a bacterial enzyme in yeast to achieve increased thermostability, directly addressing that claim limitation.

4. Key Claim Construction Positions

  • Petitioner argued that even under its proposed narrower constructions, the claims are unpatentable.
  • "appA polynucleotide": Petitioner proposed this term be limited to the specific E. coli gene identified by GenBank accession number M58708, as referenced in the patent’s specification.
  • "AppA phytase": Petitioner proposed this term be limited to a phytase isolated from wild-type E. coli encoded by the appA polynucleotide, not any phytase merely "derived" from it.
  • Petitioner contended that because the prior art discloses these specific, narrower embodiments, proving unpatentability under this narrow scope necessarily proves it under the Patent Owner’s broader proposed constructions.

5. Arguments Regarding Discretionary Denial

  • Petitioner argued that the grounds presented were not cumulative of issues considered by the USPTO during prosecution of the ’150 patent. It was asserted that the examiner never considered the specific prior art combinations presented in the petition. For instance, the examiner did not previously consider Kretz in combination with Cheng, nor Greiner's disclosure of phytase activity in combination with an efficient yeast expression system. Furthermore, Petitioner argued that the applicant overcame prior rejections by arguing that increased thermostability in yeast was unexpected, a position directly contradicted by prior art like Olsen, which was not previously evaluated by the examiner in this context.

6. Relief Requested

  • Petitioner requested the institution of an inter partes review and the cancellation of claims 1-4, 6-9, 21, 28-34, and 39 of the ’150 patent as unpatentable under 35 U.S.C. §103.