Case 1:22-cv-00311-WCB Document 344 Filed 02/02/24 Page 1 of 31 PageID #: 22112
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`IN THE UNITED STATES DISTRICT COURT
`FOR THE DISTRICT OF DELAWARE
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`IMPOSSIBLE FOODS INC.,
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`Plaintiff,
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`v.
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`MOTIF FOODWORKS, INC., and
`GINKGO BIOWORKS, INC.,
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`Defendants.
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`Civil Action No. 22-311-WCB
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`JURY TRIAL DEMANDED
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`DEFENDANT MOTIF FOODWORKS, INC.’S
`ANSWERING CLAIM CONSTRUCTION BRIEF
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`Confidential Version Filed: January 26, 2024
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`PUBLIC VERSION
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`Public Version Filed: February 2, 2024
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`Case 1:22-cv-00311-WCB Document 344 Filed 02/02/24 Page 2 of 31 PageID #: 22113
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`
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`I.
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`II.
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`TABLE OF CONTENTS
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`Page
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`INTRODUCTION.................................................................................................................... 4
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`TERMS FOR CONSTRUCTION ........................................................................................... 4
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`A.
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`Term 1: “Promoter Element” ..................................................................................... 4
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`1.
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`2.
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`“Promoter Element” Is Indefinite ................................................................... 5
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`If “Promoter Element” Is Not Indefinite, “Element” Renders
`“Promoter Element” Means-Plus-Function ................................................... 9
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`B.
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`Terms 2-3: “Mxr1” Terms ........................................................................................ 10
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`1.
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`Term 2.A Refers to the Mxr1 Protein, Not to Its Binding Site .................. 12
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`(a)
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`(b)
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`The Claims and Intrinsic Record Support Defendants ................... 12
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`Impossible’s Remaining Arguments Are Unpersuasive ................ 15
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`Each Mxr1 Term Refers to the Sequence Encoding Native Mxr1............. 16
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`Motif’s Construction Should Be Adopted ................................................... 18
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`2.
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`3.
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`Term 4: “Wherein the Recombinant Nucleic Acid Molecule Comprises
`[x], Wherein the Recombinant Nucleic Acid Molecule Comprises [y]” ................ 19
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`Term 5: “A Nucleic Acid Molecule Encoding [x] and [y]” .................................... 21
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`Term 6: “Sequence to Which [the/a] Mxr1 Transcriptional Activator
`Binds” ......................................................................................................................... 23
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`Term 7: “Wherein Each Nucleic Acid Is Operably Linked to a Methanol-
`Inducible Promoter Element”.................................................................................... 25
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`Term 8: “wherein the [methanol-inducible] promoter element” / “wherein
`the [at least one] methanol-inducible promoter element” ....................................... 27
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`C.
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`D.
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`E.
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`F.
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`G.
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`III.
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`CONCLUSION ...................................................................................................................... 27
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`i
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`Case 1:22-cv-00311-WCB Document 344 Filed 02/02/24 Page 3 of 31 PageID #: 22114
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`
`
`TABLE OF AUTHORITIES
`
`Cases
`
`Page(s)
`
`Becton, Dickinson & Co. v. Tyco Healthcare Grp., LP,
`616 F.3d 1249 (Fed. Cir. 2010) ............................................................................................... 5, 12
`
`Convolve, Inc. v. Compaq Comput. Corp.,
`812 F.3d 1313 (Fed. Cir. 2016) ................................................................................................... 24
`
`Eli Lilly & Co. v. Teva Pharms. USA, Inc.,
`619 F.3d 1329 (Fed. Cir. 2010) ............................................................................................. 10, 11
`
`Finjan LLC v. SonicWall, Inc.,
`84 F.4th 963 (Fed. Cir. 2023) ...................................................................................................... 24
`
`Geneva Pharm., Inc. v. GlaxoSmithKline PLC,
`349 F.3d 1373 (Fed. Cir. 2003) ................................................................................................... 11
`
`Icon Health & Fitness, Inc. v. Polar Electro Oy,
`656 F. App’x 1008 (Fed. Cir. 2016) .......................................................................................... 3, 4
`
`Intel Corp. v. Qualcomm Inc.,
`21 F.4th 801 (Fed. Cir. 2021) ........................................................................................................ 5
`
`IQASR LLC v. Wendt Corp.,
`825 Fed.Appx. 900 (Fed. Cir. 2020) ......................................................................................... 4, 5
`
`Iridescent Networks, Inc. v. AT&T Mobility, LLC,
`933 F.3d 1345 (Fed. Cir. 2019) ..................................................................................................... 4
`
`Kyocera Senco Indus. Tools Inc. v. Int’l Trade Comm’n,
`22 F.4th 1369 (Fed. Cir. 2022) .................................................................................................... 12
`
`Massachusetts Inst. of Tech. & Elecs. For Imaging, Inc. v. Abacus Software,
`462 F.3d 1344 (Fed. Cir. 2006) ..................................................................................................... 6
`
`Microprocessor Enhancement Corp. v. Tex. Instruments Inc.,
`520 F.3d 1367 (Fed. Cir. 2008) ................................................................................................... 19
`
`New Hampshire v. Maine,
`532 U.S. 742 (2001) ..................................................................................................................... 18
`
`Personalized Media Commc’ns, LLC v. Int’l Trade Com’n,
`161 F.3d 696 (Fed. Cir. 1998) ....................................................................................................... 6
`
`
`
`ii
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`

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`Case 1:22-cv-00311-WCB Document 344 Filed 02/02/24 Page 4 of 31 PageID #: 22115
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`
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`Traxcell Techs., LLC v. Nokia Sols. & Networks Oy,
`15 F.4th 1136 (Fed. Cir. 2021) .................................................................................................... 24
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`Trustees in Bankr. of N. Am. Rubber Thread Co. v. United States,
`593 F.3d 1346 (Fed. Cir. 2010) .......................................................................... 17, 18, 19, 21, 25
`
`Trustees of Columbia Univ. in City of New York v. NortonLifeLock, Inc.,
`No. 3:13CV808, 2019 WL 7040931 (E.D. Va. Dec. 20, 2019) ............................. 18, 19, 21, 25
`
`Williamson v. Citrix Online, LLC,
`792 F.3d 1339 (Fed. Cir. 2015) (en banc) .............................................................................. 7, 22
`
`X One, Inc. v. Uber Techs., Inc.,
`440 F. Supp. 3d 1019 (N.D. Cal. 2020) ...................................................................................... 19
`
`
`
`
`
`iii
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`Case 1:22-cv-00311-WCB Document 344 Filed 02/02/24 Page 5 of 31 PageID #: 22116
`Case 1:22-cv-00311-WCB Document 344 Filed 02/02/24 Page 5 of 31 PagelD #: 22116
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`I.
`
`INTRODUCTION
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`The Court should adopt Motif’s proposed constructions, which are consistent with the
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`interpretations proffered by co-defendant Ginkgo, for U.S. Patent Nos. 10,273,492 ("492 patent”, Ex.
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`1) and 10,689,656 (“656 patent”, Ex. 2) (the “Yeast Patents”).
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`Motif explains why a person skilled in the art of the Yeast Patents (“POSA”) would not be
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`able to reasonably ascertain the boundaries of certam terms in light of the patents’ murky
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`specifications and the absence of consistent art-accepted terminology. Motifs other proffered
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`constructions are groundedin the intrinsic record, the knowledge of a POSA and Impossible’s own
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`interpretations advanced in related proceedings.
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`By contrast, Impossible’s litigation-driven interpretations find no support in the intrinsic
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`record or a POSA’s understanding and should be rejected. Impossible should also be held to its prior
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`interpretations ofthese terms, which resulted in the Patent Trial and Appeal Board (“PTAB”) denying
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`Motif’s interpartes review challenges to the Yeast Patents.
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`Il.
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`TERMS FOR CONSTRUCTION
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`A.
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`Term 1: “Promoter Element”
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`indefinite
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`expression All asserted claims
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`something that modulates, directs or regulates
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`No party contends that the term “promoter,” standing alone,is indefinite but the definition of
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`that term is not at issue in these proceedings. Impossible could have but did not define its invention
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`by drafting claims reciting simply a “promoter,” or even specific sequences found in promoters.
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`Instead, Impossible drafted each ofthe asserted claims to cover a “promoter element,” which the Yeast
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`Patents make clear is something different from a complete promoter. However, Impossible did not
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`4
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`Case 1:22-cv-00311-WCB Document 344 Filed 02/02/24 Page 6 of 31 PageID #: 22117
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`define or provide any description in the patents about what part—much less specific sequences—of a
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`promoter constitutes an “element.”
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`The parties’ dispute thus turns on whether (or how) a POSA would understand, without any
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`description or direction in the patents, what the modifier “element” means in reference to a
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`“promoter.”
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`1.
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`“Promoter Element” Is Indefinite
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`As Motif previously argued, a POSA would not be reasonably certain of the scope of
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`“promoter element” as recited in the Yeast Patent claims. D.I. 120, 25-27; D.I. 148, 8-9. The
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`specification makes clear that a “promoter element” is some quantum of a promoter—not a full
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`promoter itself. D.I. 120, 26; Ex. 2, ’656 patent, 4:52-5:11 (reciting promoters “or a promoter element
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`therefrom”); 6:28-51 (similar); 6:57-61 (similar). Impossible’s prior contention that a “promoter
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`element” “can be an entire promoter sequence” is plainly wrong. D.I. 114, 15.
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`Neither the claims nor the specification define what portion or specific sequences of a
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`promoter provides the function(s) of the claimed “promoter element.” D.I. 120, 25-27; D.I. 148, 8-9.
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`Lacking a definition, Impossible contends that “promoter element” is “a type of expression element”
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`and means a “nucleic acid sequence that directs or regulates transcription of downstream genes.” D.I.
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`114, 15.
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`This only muddies the waters further. The Yeast Patents do not specify any structural features
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`or specific sequence(s) that define an “expression element.” They do not provide any other
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`benchmarks for what quantum of a promoter falls within—or does not fall within—the scope of
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`“promoter element.”
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`Nor do the patents describe any structural metes and bounds for the function Impossible
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`alleges is performed by a “promoter element.” Contrary to Impossible’s prior positions, for example,
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`a “promoter element” does not necessarily contain a Mxr1 binding site. See D.I. 142, 14-15. This is
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`5
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`Case 1:22-cv-00311-WCB Document 344 Filed 02/02/24 Page 7 of 31 PageID #: 22118
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`shown in the Yeast Patent claims. Claims 1 of the ’492 patent recites (twice) “a promoter element
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`from P. pastoris,” and dependent claim 5 recites that “the promoter element from P. pastoris” can be
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`“a methanol-inducible promoter element.” Contrast those claims with claim 1 of the ’656 patent,
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`which recites “at least one methanol-inducible promoter element comprising a sequence to which the
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`Mxr1 transcriptional activator binds.” A “promoter element” therefore can contain a Mxr1 binding
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`site, but that binding site is not a required feature. “Promoter elements” can also have different
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`activities (e.g., they can be “constitutive” or “inducible,” see ’492 patent claim 5), requiring different
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`structural features. D.I. 123, ¶¶153-155.
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`A POSA would not be reasonably certain of the scope of a “promoter element” based on the
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`varied and indiscriminate use of that term in the technical literature.1 Outside of the context of a full
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`promoter, the term “promoter element” has no established, consistent, or understood meaning. D.I.
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`123, ¶135. Rather, the meaning of this term depends on the subjective whims of individual scientists.
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`A POSA would not know, for example, whether a “promoter element” means merely that a few
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`nucleotides in a promoter sequence have been changed, id., ¶¶166-172, or whether it refers to very
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`small sequences—e.g., the familiar four-nucleotide “TATA box”—that is present in the promoters of
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`nearly all higher-order organisms. Id. ¶¶156-158.
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`A scientist’s individual use of “promoter element” might be apparent within the four corners
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`of a research article, which is not the case with the Yeast Patents. But terms may be indefinite if they
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`are “relative terms” which “only have meaning in a given context with a defined reference.” Icon
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`Health & Fitness, Inc. v. Polar Electro Oy, 656 F. App’x 1008, 1015 (Fed. Cir. 2016). Here,
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`1 In a declaration accompanying this brief (“Lin-Cereghino”), Motif’s expert Dr. Geoffrey
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`Lin-Cereghino explains his agreement with Dr. Batt’s opinions. Lin-Cereghino §VIII.A.
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`6
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`Case 1:22-cv-00311-WCB Document 344 Filed 02/02/24 Page 8 of 31 PageID #: 22119
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`“promoter element” is indefinite because it is a “moving target” for which “the scope could vary from
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`day-to-day and from person-to-person.” Id. at 1016.
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`Impossible and its expert never showed otherwise. “When a term ‘has no ordinary and
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`customary meaning,’ it is a ‘coined term,’ raising the question of ‘whether the intrinsic evidence
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`provides objective boundaries to the scope of the term.” IQASR LLC v. Wendt Corp., 825 Fed.Appx.
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`900, 904 (Fed. Cir. 2020) (quoting Iridescent Networks, Inc. v. AT&T Mobility, LLC, 933 F.3d 1345,
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`1353 (Fed. Cir. 2019)).
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`
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`IQASR is instructive because the patentee asserted that the claim term at issue was defined
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`based on other technical terms. 825 F. App’x at 905 (“[T]o discern ‘magnetic fuzz,’ an artisan has to
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`find the low susceptance microparticles, and then identify which low susceptance microparticles are
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`disassociated magnetically active microparticles.”). Similarly, Impossible tries to define “promoter
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`element” by pointing to the patents’ description of a different term, “expression elements.” D.I. 114,
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`15. But “expression element” is also undefined. The patents merely provide several examples of
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`what different “expression elements” can be. Ex. 2, 9:66-10:5. A “promoter element” is not among
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`that list.
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`Recognizing that “expression element” does not provide sufficient context to define “promoter
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`element,” Impossible points to another term, “operably linked,” which is defined to mean “a promoter
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`or other expression element(s) are positioned relative to a nucleic acid coding sequence in such a way
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`as to direct or regulate expression of the nucleic acid (e.g., in-frame).”) (emphasis added).” D.I.
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`114, 15; Ex. 2, 4:48-51.
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`Under its interpretation, Impossible effectively reads “operably linked” out of the claim while
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`giving no definition or explanation of what constitutes a “promoter element.” This interpretation runs
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`afoul of the principle that claims must be “interpreted with an eye toward giving effect to all terms in
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`the claim.” Becton, Dickinson & Co. v. Tyco Healthcare Grp., LP, 616 F.3d 1249, 1257 (Fed. Cir.
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`7
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`Case 1:22-cv-00311-WCB Document 344 Filed 02/02/24 Page 9 of 31 PageID #: 22120
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`2010). Impossible’s construction renders “operably linked” superfluous. Such an approach is “highly
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`disfavored” and should be rejected. Intel Corp. v. Qualcomm Inc., 21 F.4th 801, 809-10 (Fed. Cir.
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`2021) (rejecting construction of “buffer implemented in hardware” for term “hardware buffer”
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`because if the former does not “mean something more,” “the word ‘hardware’ would be erased from
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`the claims”).
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`Here, as in IQASR, “because the multiple layers of definitions are all open-ended and non-
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`limiting, a skilled artisan must wade through a morass of uncertainty and contradiction ” and “word
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`salad of inconsistent indirect definitions.” 825 F. App’x at 905. A POSA would thus not be able to
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`reasonably ascertain the boundaries of when something “is or is not” a “promoter element.” Id. at
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`907.
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`Nothing in Impossible’s prior briefing supports a different conclusion. Indeed, Impossible
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`contends that “promoter elements” are “those elements of the promoter that are meaningful” in the
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`context of the claims. D.I. 142 at 13-14 (emphasis added). This nebulous assertion merely
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`underscores the subjectivity of Impossible’s construction. That Impossible’s expert “managed to
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`articulate a definition” for “promoter element” is irrelevant because, in relying only on cherry-picked
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`parts of the patents’ murky description, he failed to “translate the definition into meaningfully precise
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`claim scope.” IQASR, 825 F. App’x at 907.
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`To the extent Impossible argues that Motif took a different position in IPR proceedings,
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`Impossible is wrong. Motif’s interpretation of “promoter element” is fully consistent with Motif’s
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`position in IPR proceedings regarding the Yeast Patents, where Motif’s expert mapped the “promoter
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`element” limitations to full promoter sequences (which necessarily contain all elements of the
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`promoter) present in the prior art without taking a position on what portion of the prior art promoters
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`are the “promoter element.” D.I. 149, ¶¶56-59.
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`8
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`Case 1:22-cv-00311-WCB Document 344 Filed 02/02/24 Page 10 of 31 PageID #: 22121
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`2.
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`If “Promoter Element” Is Not Indefinite, “Element” Renders “Promoter
`Element” Means-Plus-Function
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`
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`“Promoter element” is indefinite. See supra. If the Court finds otherwise, this term should be
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`construed as a means-plus-function term, as Motif previously argued. D.I. 120, 27; D.I. 148, 9.
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`
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`The inclusion of “element” changes the meaning of a “promoter” from an understood structure
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`into an unbounded, murky concept as explained above. However, the term “element” does not
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`introduce any additional structure that would define or clarify the scope of the “promoter element”
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`term. As the Federal Circuit has recognized, “[t]he “generic term[] … ‘element,’ … typically do[es]
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`not connote sufficiently definite structure” to save a term from means-plus-function construction.
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`Massachusetts Inst. of Tech. & Elecs. For Imaging, Inc. v. Abacus Software, 462 F.3d 1344, 1354
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`(Fed. Cir. 2006) (“We contrasted the term ‘detector,’ which recited sufficient structure to avoid 112 ¶
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`6, with ‘generic structural term[s] such as “means,” “element,” or “device,”’ which do not.”)
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`(emphasis added) (quoting Personalized Media Commc’ns, LLC v. Int’l Trade Com’n, 161 F.3d 696,
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`704 (Fed. Cir. 1998)). The Federal Circuit’s view aligns with the generic dictionary definition of
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`“element.” D.I. 123, ¶138.
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`It is true that the Yeast Patent claims do not recite the term “means.” However, “[w]hen a
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`claim term lacks the word ‘means,’ the presumption can be overcome and § 112, para. 6 will apply if
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`the challenger demonstrates that the claim term fails to ‘recite sufficiently definite structure’ or else
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`recites ‘function without reciting sufficient structure for performing that function.’” Williamson v.
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`Citrix Online, LLC, 792 F.3d 1339, 1349 (Fed. Cir. 2015) (en banc). Moreover, no “heightened
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`evidentiary showing” is required to overcome this presumption. Id. In fact, Williamson “expressly
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`overrul[ed both] the characterization of that presumption as ‘strong’” and the “strict requirement of a
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`showing that the limitation essentially is devoid of anything that can be construed as structure .” Id.
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`Rather, “[t]he standard is whether the words of the claim are understood by persons of ordinary skill
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`in the art to have a sufficiently definite meaning as the name for structure.” Id.
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`9
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`Case 1:22-cv-00311-WCB Document 344 Filed 02/02/24 Page 11 of 31 PagelD #: 22122
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`Here, the term “element”lacks sufficiently definite structure to avoid construction as a means-
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`plus-function term. As explained above, the patents’ specifications do not describe what makes any
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`particular structure an “element” of a promoter such that a POSA would be reasonably certain ofits
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`interpretation. A POSA’s knowledgedoesnotfill that void as “promoter element” does not have a
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`consistent meaning in the art. E.g., D.I. 123, §XI; Lin-Cereghino, §65. In fact, its meaning is wholly
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`subjective.
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`Under Impossible’s interpretation, “promoter element” is defined purely by its function—it
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`has no structure whatsoever, muchless “sufficiently definite” structure. Williamson, 792 F.3d at 1349.
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`And because this term covers something different from a “promoter,” the claims merely recite
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`“function without reciting sufficient structure for performing that function.” Jd.
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`B.
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`Terms 2-3: “Mxri” Terms
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`Claim Terms 2-3, reproduced below, contain similar language with minor variations. They
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`warrant consideration together because, as Motif previously argued, they each refer to sequencesthat
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`encode the Mxr1 protein.
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`___“Mxri”Term|Motif——|Gimkgo—|__—sImpossible
`“a Mxrl “the sequence of the|a sequence of an Mxr1|the consensus
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`transcriptional
`native P. pastoris
`transcriptional
`sequencethat
`
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`activator sequence Mxr1 transcriptional|activator protein actually binds the
`from P. pastoris”
`activator”
`[Term 2.a]
`[Mxr1] protein
`(°492 patent, cl. 1)?
`[Term 2.a]
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`x found naturally in P.
`pastoris [Term 3]
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`the sequence thatis
`associated with P.
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`pastoris [Term 3]
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`“a first exogenous a sequence of an Mxr1|the gene that makes“a first exogenous
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`
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`nucleic acid encoding|nucleic acid the [Mxrl] protein
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`a methanol expression|sequence ofa native [Term 2.b]
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`2 This term waspreviously described as Term 18 (Impossible) and Term 4 (Motif). D.I. 94-
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`1 at 8.
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`10
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`Impossible
`regulator 1 (Mxr1) Mxrl transcriptional|transcriptional
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`transcriptional
`activator”
`activator proteim
`the sequencethatis
`activator”
`[Term 2.b]
`associated with P.
`(656 patent, cl. 1)
`pastoris [Term 3]
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`x found naturally in P.
`pastoris [Term 3](cl.
`7,10, 11, 26, 28
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`pastoris [Term 3]
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`a nucleic acid a sequence of an Mxrl|the gene that makes“a nucleic acid
`
`
`encoding a Mxrl
`encoding the
`transcriptional
`the [Mxrl] protein
`transcriptional
`sequence ofthe
`activator protein
`[Term 2.c]
`activator sequence
`native P. pastoris
`[Term 2.c]
`the sequencethatis
`from P. pastoris”
`Mxr1 transcriptional
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`(656 patent, cl. 26)4 x found naturally in P.|associated with P.activator”
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`pastoris [Term 3]
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`Ginkgo addressesthe parties’ disputes over the Mxr1 Terms’ meaning by dividing them into
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`Terms 2 and 3. This approach accounts for the difference between 656 patent claim 1, which does
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`not modify the “Mxr1” term (Term 2.b) with “from P. pastoris” (Term 3), and the other independent
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`claims, which do. However, Ginkgo’s approach represents a distinction without a substantive
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`difference from Motif’s proposed constructions because, as Motif has argued, a POSA would
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`understand that all Mxrl Termsrefer to native gene sequences encoding the Mxr1 protein (some of
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`which are native to the organism P. pastoris specifically).
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`Regardless ofhow Terms 2-3 are framed, they require the Court’s construction in two respects.
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`First, the parties dispute whether Term 2.a,a term recitedin all ’492 patent claims, refers to a sequence
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`encoding the Mxr1 transcription factor protein itself or, instead, to a sequence to which the Mxrl
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`protem binds. Second, Motif understands the parties to dispute whether “Mxrl,” as recited in the
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`Mxr1 Terms,refers to “native” Mxrl sequencespresent in the respective genomesofthe species of
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`3 Previously Term 19 (Impossible), Term 4 (Motif). D.I. 94-1 at8.
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`4 Previously Term 20 (Impossible), Term 4 (Motif). D.I. 94-1 at 8.
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`11
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`Case 1:22-cv-00311-WCB Document 344 Filed 02/02/24 Page 13 of 31 PageID #: 22124
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`origin, such as the yeast P. pastoris, or whether “Mxr1” encompasses some variant thereof (and what
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`that variant might be).
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`For at least the reasons given below, the Court should adopt Motif’s interpretations of the
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`Mxr1 Terms.
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`1.
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`Term 2.A Refers to the Mxr1 Protein, Not to Its Binding Site
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`(a)
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`The Claims and Intrinsic Record Support Defendants
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`There is no dispute that the Mxr1 Terms recited in the ’656 patent claims refer to sequences
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`encoding the Mxr1 protein itself. See supra Terms 2.b-2.c. Indeed, Impossible agreed in its prior
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`briefing, pointing to the ’656 patent claims’ recitation of the term “encoding” with respect to these
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`terms. D.I. 142 (Reply) at 10 (“Motif acknowledges that ‘[t]he specification [] repeatedly describes
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`a Mxr1 nucleic acid sequence that encodes Mxr1—not a binding site.’ This is consistent with terms
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`19-20, which include the word “encoding.”) (emphasis original) (docket citations omitted).
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`Impossible contends, however, that a very similar term in the ’492 patent—“a Mxr1
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`transcriptional activator sequence from P. pastoris” (Term 2.a, previously annotated as Term 18)—
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`recites a nucleic acid sequence to which Mxr1 binds, rather than Mxr1 itself. D.I. 142 (Reply) at 10
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`(“A POSA would understand that term 18 requires an Mxr1 ‘binding site’ …”). Impossible’s
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`interpretation is inconsistent with the ’492 patent claims and intrinsic record, needlessly injects
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`ambiguity into the claims, and is inconsistent with how a POSA would interpret the Mxr1 Terms (and
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`how Impossible previously interpreted these terms). Impossible’s interpretation should be rejected.
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`For multiple reasons, a POSA would understand the ’492 patent’s “Mxr1” term (Term 2.a) to
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`mean the sequence encoding the Mxr1 protein itself, rather than a Mxr1 binding site.
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`First, the Yeast Patent specifications describe Mxr1 “sequences” as sequences encoding Mxr1
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`rather than Mxr1 binding sites. Ex. 2, 1:63-65 (“In some embodiments, the exogenous nucleic acid
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`encoding a transcriptional activator comprises a Mxr1 sequence from Pichia pastoris …”); 4:26-27
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`Case 1:22-cv-00311-WCB Document 344 Filed 02/02/24 Page 14 of 31 PageID #: 22125
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`(“For example, a transcriptional activator from Pichia pastoris is the Mxr1 sequence …”) (emphases
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`added); D.I. 123, ¶¶130-134;. In contrast, the patents do not describe “sequences” as sequences of
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`the transcription factors that bind them. D.I. 123, ¶¶130-134; Lin-Cereghino, ¶88.
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`Second, the ’492 patent’s prosecution history is consistent with Defendants’ interpretations.
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`As explained in Ginkgo’s brief, an analogous term in the ’327 sister patent’s claims can be the
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`sequence encoding the Mxr1 protein. D.I. 333, 8-9 (analyzing ’327 patent claims 1 and 17).
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`Consistent with Ginkgo’s position, the ’492 patent claims were rejected for non-statutory
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`double patenting over the then-pending ’327 patent claims. Ex. 3, File History of U.S. Appl. No.
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`15/678,342, Final Rejection dated June 13, 2018, at 3. This rejection further supports Defendants’
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`interpretation because non-statutory double patenting “precludes more than one patent on the same
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`invention.” Eli Lilly & Co. v. Teva Pharms. USA, Inc., 619 F.3d 1329, 1341 (Fed. Cir. 2010)
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`(emphasis added) (quoting Geneva Pharm., Inc. v. GlaxoSmithKline PLC, 349 F.3d 1373, 1377-78
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`(Fed. Cir. 2003)). The doctrine of non-statutory double patenting bars “claims that ‘vary slightly from
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`the earlier patent’ … to prevent issuance of a patent on claims that are nearly identical to claims in an
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`earlier patent.’” Id.
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`The ’492 patent’s prosecution history shows that the Patent Office viewed the pending ’492
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`patent claims as “a ‘slight variant’ from the claims in the earlier” ’327 patent. See 619 F.3d at 1341.
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`This is consistent with Defendants’ interpretation that the Term 2.a Mxr1 Term recites the sequence
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`that encodes Mxr1, not a sequence to which Mxr1 binds.
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`Third, at the PTAB, Impossible did not urge that Term 2.a should be construed as a binding
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`site instead of a sequence encoding Mxr1. Ex. 4, Patent Owner Preliminary Response, IPR2023-
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`00322, (May 9, 2023), at 2 (“Patent Owner submits that no constructions are needed for the Board to
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`reach a decision denying institution.”).
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`Case 1:22-cv-00311-WCB Document 344 Filed 02/02/24 Page 15 of 31 PageID #: 22126
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`Nor did the PTAB interpret this term to recite a Mxr1 binding site rather than Mxr1 itself. Ex.
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`5, Institution Decision, IPR2023-00322, (Aug. 7, 2023), at 7 (“[N]o claim terms need to be construed
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`to resolve any controversies in dispute.”). Rather, the PTAB analyzed Term 2.a consistently with
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`Motif’s challenge—e.g., as “the nucleic acid sequence encoding Mxr1 under control of the promoter
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`element PGAP to regulate PAOX1 controlled expression of the hemoprotein to arrive at the nucleic acid
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`recited in claim element 1[a].” Id. at 11 (emphasis added).
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`Fourth, Impossible’s construction, if adopted, would render the claim fatally ambiguous. ’492
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`patent claim 1 recites:
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`A methylotrophic Pichia yeast cell comprising:
`a nucleic acid molecule encoding a heme-containing protein operably linked to a
`promoter element from P. pastoris and a Mxr1 transcriptional activator sequence from
`P. pastoris; and
`a nucleic acid molecule encoding at least one polypeptide involved in heme
`biosynthesis operably linked to a promoter element from P. pastoris and a Mxr1
`transcriptional activator sequence from P. pastoris.
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`In drafting, Impossible included two distinct elements: the “promoter element” (blue) and the
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`Mxr1 Term (red). When claim terms are listed separately, there is “a presumption that those
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`components are distinct.” Kyocera Senco Indus. Tools Inc. v. Int’l Trade Comm’n, 22 F.4th 1369,
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`1382 (Fed. Cir. 2022); Becton, Dickinson & Co. v. Tyco Healthcare Grp., LP, 616 F.3d 1249, 1254
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`(Fed. Cir. 2010) (“Where a claim lists elements separately, ‘the clear implication of the claim
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`language’ is that those elements are ‘distinct component[s]’ of the patented invention.”). Thus, the
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`blue portions of the ’492 patent claims are presumptively distinct from the Mxr1 Terms (red).
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`As a result, under Impossible’s interpretation of Term 2.a, Mxr1 binding sites (e.g., the red
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`element) must be something different from the promoter element (e.g., the blue element). Lin-
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`Cereghino, ¶¶77-86. However, a POSA would not be reasonably certain from the Yeast Patent claims
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`or specification what the scope of “something different” might be. Id. For example, if a “promoter
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`element” is construed functionally as Impossible proposes but it also is something different from a
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`Case 1:22-cv-00311-WCB Document 344 Filed 02/02/24 Page 16 of 31 PageID #: 22127
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`binding site (the consequence of Impossible’s construction of Term 2.a), then it is wholly unclear
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`what structures or features that “something different” could conceivably include. See id.
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`Had Impossible sought to claim a sequence to which Mxr1 binds in addition to the separate
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`“promoter element” term (blue), it could have used unambiguous terminology such as “bind.” E.g.,
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`Ex. 2, 5:18-21 (“[T]he methanol-regulated transcriptional activators in Pichia can bind to the AOX1
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`promoter…”) (emphasis added). It also could have claimed specific promoter sequences. Id., 4:60-
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`5:11 (listing promoters reported in literature or available at “GenBank Accession No.[s]”).
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`Impossible did not do so. The claim’s recitation of “sequence” is the sequence encoding Mxr1
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`as explained above.
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`(b)
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`Impossible’s Remaining Arguments Are Unpersuasive
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`Each of Impossible’s contrary arguments fail. First, the Yeast Patents do not describe a
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`consensus sequence. E.g., Lin-Cereghino, ¶119. Neither this term nor any consensus sequence
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`appears in the specification. Id., ¶88.
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`Second, assuming Impossible reiterates its argument from prior briefing, Impossible’s
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`argument is premised entirely on its observation that, unlike the ’656 patent claims, the ’492 patent
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`claims do not expressly recite a sequence “encoding” Mxr1. See D.I. 142, 10; see also D.I. 144, ¶¶6,
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`8, 10.
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`From this drafting choice in a different patent, Impossible concludes that the nature of the
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`recited “sequence” is entirely different. This conclusion is unsupported. There is no independent
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`support in the claims or intrinsic record for Impossible’s construction of Term 2.a as a “consensus”
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`sequence rather than an encoding sequence, and Impossible identifies none.
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`Thir