Case 1:22-cv-00311-WCB Document 414 Filed 03/22/24 Page 1 of 28 PageID #: 25195
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`IN THE UNITED STATES DISTRICT COURT
`FOR THE DISTRICT OF DELAWARE
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`Civil Action No. 22-311-WCB
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`FILED UNDER SEAL
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`IMPOSSIBLE FOODS INC.,
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`Plaintiff,
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`MOTIF FOODWORKS, INC., and
`GINKGO BIOWORKS, INC.,
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`v.
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`Defendants.
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`CLAIM CONSTRUCTION ORDER
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`In this patent case, plaintiff Impossible Foods Inc. has asserted numerous claims from U.S.
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`Patent No. 10,273,492 (“the ’492 patent”) and U.S. Patent No. 10,689,656 (“the ’656 patent”)
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`against defendants Motif Foodworks, Inc. and Gingko Bioworks, Inc.1 The asserted patents are
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`directed to the expression of heme-containing proteins in genetically engineered yeast, as well as
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`other proteins that assist in that goal.
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`The parties disagree about the proper construction of a number of claim terms from the
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`asserted patents.2 They have filed numerous briefs outlining their positions with respect to each
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`disputed term. Dkt. Nos. 106, 120, 142, 148, 333, 338, 340, 346, 351, 352. Several of those briefs,
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`1 Impossible has also asserted claims against Motif from Impossible’s U.S. Patent Nos.
`9,943,096; 10,039,306; 10,863,761; 11,013,250; and 11,224,241, which are directed to food
`products designed to mimic the taste of meat. On July 24, 2023, I ordered the portion of the case
`involving Impossible’s claims of infringement of the food product patents to be tried separately
`from the portion of the case involving Impossible’s claims of infringement of the yeast patents.
`Dkt. No. 161 at 1. Although I characterized that action as a “severance of the two cases,” it is
`more properly characterized as an order providing for separate trials for claims found in the two
`groups of patents, pursuant to Rule 43 of the Federal Rule of Civil Procedure. In this order I have
`addressed only the claim construction issues relating to the yeast patents.
`2 The parties have provided competing approaches for numbering the disputed claim terms.
`For simplicity, I have adopted Ginkgo’s system of numbering the claim terms.
`1
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`Case 1:22-cv-00311-WCB Document 414 Filed 03/22/24 Page 2 of 28 PageID #: 25196
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`Dkt. Nos. 106, 120, 142, and 148, were filed prior to my order directing that the yeast patent claims
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`be tried separately from the food product claims. Those briefs address terms from the food
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`products patents as well as from the yeast patents. Dkt. Nos. 333, 338, 340, 346, 351, and 352
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`address only terms from the yeast patents. On March 18, 2024, I held a claim construction hearing.
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`I address below each of the disputes identified in the parties’ briefing and at the hearing.
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`Term 1: “Promoter Element”
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`The first term disputed by the parties is “promoter element,” which is found in all the
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`asserted claims. Impossible argues that a “promoter element” is a polynucleotide that regulates
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`transcription of another polynucleotide sequence. Impossible further argues that the promoter
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`element is upstream of, and adjacent to the gene.
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`Ginkgo and Motif argue that the term “promoter element” is indefinite. To avoid invalidity
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`for indefiniteness, a patent claim must “inform, with reasonable certainty, those skilled in the art
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`about the scope of the invention.” Nautilus, Inc. v. Biosig Instruments, Inc., 572 U.S. 898, 901
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`(2014). Indefiniteness is a question of law dependent on subsidiary questions of fact. Teva
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`Pharms. USA, Inc. v. Sandoz, Inc., 574 U.S. 318, 325 (2015). The meaning to a person of ordinary
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`skill in the art of “technical words or phrases not commonly understood” is one such factual
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`question. Id. at 326.
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`“Promoter” is a term of art. It refers to a portion of a gene with binding sites for
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`transcriptional activators to bind and regulate gene expression. Dkt. No. 341 at ¶ 62. The claim
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`term, however, is “promoter element,” and “promoter element” is not a term of art.3 As used in
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`3 Impossible’s expert, Dr. Hal Alper, argues that “promoter element” is a term of art, and
`in support he cites two articles referring to a “promoter element.” Dkt. No. 339 at ¶ 27. The two
`articles he cites, however, both use “promoter element” to mean “promoter.” A promoter is one
`element of a gene, which is why the articles Dr. Alper cites refer to the promoter portion of the
`gene as a “promoter element.”
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`2
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`Case 1:22-cv-00311-WCB Document 414 Filed 03/22/24 Page 3 of 28 PageID #: 25197
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`the asserted claims, the term “promoter element” refers to a part of a promoter sequence. Put
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`differently, a promoter element is simply an element of a promoter. The specification4 makes clear
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`that a “promoter element” is part of a promoter by repeatedly referencing a “promoter or promoter
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`element therefrom” and equating that phrase to a “promoter, or a portion thereof.” ’656 patent at
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`4:54–60; see also id. at 7:5–6 (“[A] single promoter, or promoter element therefrom can be used
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`to drive transcription . . . .”); id. at 6:60–61 (“Other methanol-inducible promoter elements
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`therefrom, however, can be used . . . .”). Ginkgo and Motif concede that a promoter element is
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`part of a promoter, Dkt. No. 333 at 3; Dkt. No. 340 at 5, so this aspect of the term is not at issue.
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`Ginkgo and Motif argue, however, that a person of ordinary skill in the art would not know
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`which parts of a promoter would constitute a promoter element. In other words, they assume that
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`only certain parts of a promoter can constitute a promoter element, and that the failure to identify
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`which parts of the promoter contribute the promoter element renders the claims indefinite.
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`The intrinsic record does not expressly state which parts of a promoter constitute a
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`promoter element, but it describes the characteristics of a promoter element. Namely, it makes
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`clear that a promoter element must be able to perform the functions of a promoter. For example,
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`the specification of the ’656 patent describes the use of a specific methanol-inducible promoter
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`that is “strongly transcribed in response to methanol.” ’656 patent at 4:56–60. It goes on to
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`explain that the specific promoter can be substituted for other methanol-inducible promoters or
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`promoter elements therefrom with similar characteristics. ’656 patent at 4:60–5:11. Thus, a
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`“promoter element” is a part of a promoter capable of performing the functions of a promoter.
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`4 The specifications of the two patents in suit are almost identical. Accordingly, statements
`in this opinion regarding the specification refer to the common language in each of the
`specifications.
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`3
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`Although “promoter element” may be an imprecise term, it is not indefinite, as Ginkgo and
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`Motif argue. “[A] patentee need not define his invention with mathematical precision in order to
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`comply with the definiteness requirement.” Niazi Licensing Corp. v. St. Jude Med. S.C., Inc., 30
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`F.4th 1339, 1347 (Fed. Cir. 2022) (quoting Guangdong Alison Hi-Tech Co. v. Int'l Trade Comm'n,
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`936 F.3d 1353, 1359 (Fed. Cir. 2019). It is not necessary, therefore, that the patents delineate
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`exactly what portion of a promoter can constitute a promoter element. All that is required is that
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`the term reasonably inform a person of ordinary skill in the art about the scope of the invention.
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`Nautilus, 572 U.S. at 901.
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`A person of ordinary skill in the art would certainly understand that the term “promoter
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`element” covers a full promoter. Dr. Carl Batt, for example, one of Motif and Ginkgo’s technical
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`experts, identified the AOX1, TEF1, and GAP promoters as promoter elements. Dkt. No. 142-1,
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`Ex. 23 at ¶¶ 44–45, 141–144. Likewise, a person of ordinary skill in the art would understand that
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`a short, dysfunctional, region of the promoter would not be a promoter element within the meaning
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`of the claims, even if it were taken from a promoter, because such a sequence could not be used in
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`the ways contemplated by the specification. As such, a person of ordinary skill would have a
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`reasonable understanding of the scope of the invention. Here, “the language is as precise as the
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`subject matter permits,” so the term is not indefinite. PPG Industries, Inc. v. Guardian Industries
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`Corp., 75 F.3d 1558, 1562–63 (Fed. Cir. 1996).
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`Although I agree with Impossible’s indefiniteness position, Impossible’s proposed
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`construction of “promoter element” reads in definitions from other patents, which define a
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`promoter element as something that “stimulates transcription but constitutes a sub-fragment of a
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`larger promoter sequence.” Dkt. No. 339 at ¶ 28; see also id. at ¶ 29 (referring to unrelated U.S.
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`Patent No. 9,133,463, which uses “promoter element” interchangeably with “promoter” to require
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`4
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`Case 1:22-cv-00311-WCB Document 414 Filed 03/22/24 Page 5 of 28 PageID #: 25199
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`regulation of transcription). Based on the use of definitions found in other patents, Impossible
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`arrived at a proposed construction requiring that the promoter element “regulates (e.g., drives)
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`transcription.” Nothing in the intrinsic record supports the degree of specificity associated with
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`that additional limitation.
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`I therefore reject both sides’ positions and construe “promoter element” to mean “a
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`functional part of a promoter.”
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`Term 2a: “A Mxr1 transcriptional activator sequence”
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`The second term the parties address is “a Mxr1 transcriptional activator sequence,” which
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`appears in all the claims of the ’492 patent. In the absence of context, an “Mxr1 transcriptional
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`activator sequence” could mean either of two things. Because every protein is translated from a
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`DNA sequence, one potential meaning of “a Mxr1 transcriptional activator sequence” is a nucleic
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`acid sequence encoding the Mxr1 protein itself.5 In addition to being translated from a DNA
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`sequence, however, a transcriptional activator such as Mxr1 also binds to different DNA sequences
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`from the ones that encode the Mxr1 protein. Thus, the second potential meaning of “a Mxr1
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`transcriptional activator sequence” is a DNA sequence to which Mxr1 binds. Ginkgo and Motif
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`argue for the first meaning. Impossible argues for the second. Impossible’s construction is correct.
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`The first part of claim 1 of the ’492 patent recites “a nucleic acid molecule encoding a
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`heme-containing protein operably linked to a promoter element from P. pastoris and a Mxr1
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`transcriptional activator sequence from P. pastoris.” Under Impossible’s construction, that part of
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`claim 1 calls for a DNA sequence encoding a heme-containing protein operably linked to a
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`promoter element and an Mxr1 binding site. One role of a promoter is to bind transcription factors
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`5 Nucleic acids (DNA and RNA) use three base-pair long “codons” to encode each amino
`acid. Multiple codons will correspond with the same amino acid, so various combinations of
`codons will result in the same amino acid sequence. Thus, many different nucleic acid sequences
`can encode the same protein.
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`5
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`such as Mrx1, so an Mxr1 binding site would be on the promoter element in most embodiments.
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`A visual representation of the first nucleic acid sequence called for by claim 1 under Impossible’s
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`construction is shown below:
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`Under Ginkgo and Motif’s construction,6 the first part of claim 1 of the ’492 patent calls for a
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`heme-containing protein operably linked to a promoter element, and a sequence encoding an Mxr1
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`protein. A visual representation of the first DNA sequence called for by claim 1 under Ginkgo
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`and Motif’s constructions is shown below:7
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`
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`Although Ginkgo and Motif present reasonable arguments favoring their position, a skilled
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`artisan would not understand their construction to be correct for two reasons. First, the claims are
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`directed to the invention described in the specification under Impossible’s construction, but not
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`under Ginkgo and Motif’s. Second, Impossible’s construction makes more sense in context,
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`particularly when considering the dependent claims. Therefore, as explained in more detail below,
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`6 Ginkgo and Motif propose differently worded constructions that carry the same meaning.
`Because they are equivalent for purposes of this analysis, I treat Ginkgo and Motif’s construction
`as singular.
`7 Ginkgo and Motif’s construction does not expressly call for a second promoter and
`terminator. I have included them in the figures and annotations because they are the most standard
`way of ensuring that the DNA sequence is translated into two separate proteins, rather than a single
`dysfunctional construct. See, e.g., ’492 patent at Figure 2 (showing each coding region under a
`separate promoter). The inclusion of those additional elements does not affect any of the analysis
`in this section.
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`6
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`

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`Case 1:22-cv-00311-WCB Document 414 Filed 03/22/24 Page 7 of 28 PageID #: 25201
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`the court construes the term “a Mxr1 transcriptional activator sequence” to mean “a DNA sequence
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`to which the Mxr1 transcriptional activator protein binds.”
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`A. The Patented Invention
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`Impossible’s construction is consistent with what is described in the figures and the
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`specification of the ’492 patent, whereas Ginkgo and Motif’s construction is not. Put differently,
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`if Impossible’s construction is applied, the claims cover only what was actually invented. Figures
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`2 and 4 of the ’492 patent depict embodiments consistent with Impossible’s construction, and the
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`claims, as construed by Impossible, correspond exactly with those figures. By contrast, the
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`specification discloses no embodiments following Ginkgo and Motif’s construction. “[I]n case of
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`doubt or ambiguity it is proper in all cases to refer back to the descriptive portions of the
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`specification to aid in solving the doubt or in ascertaining the true intent and meaning of the
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`language employed in the claims.” Phillips v. AWH Corp., 415 F.3d 1303, 1315 (Fed. Cir. 2005)
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`(quoting Bates v. Coe, 98 U.S. 31, 38 (1878)). The fact that the specification aligns with the claims
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`under Impossible’s construction, but not Ginkgo’s or Motif’s, strongly suggests that Impossible’s
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`construction is correct.
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`Figure 2 of the ’492 patent depicts five plasmids (circular pieces of DNA) each containing
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`an “AOX1 promoter.” The AOX1 promoter has six binding sites for Mxr1, see Dkt. No. 334 at
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`¶ 128, which are “Mxr1 transcriptional activator sequence[s]” under Impossible’s construction.
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`Because it is a full promoter, AOX1 necessarily includes a promoter element. In other words, the
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`AOX1 promoter is one embodiment of the claimed “promoter element from P. pastoris and []
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`Mxr1 transcriptional activator sequence. . . .” Under Impossible’s construction, the plasmids in
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`Figures 2 and 4 of the asserted patents depict various embodiments of the ’492 claims. Under
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`Ginkgo and Motif’s construction, on the other hand, none of the embodiments in the specification
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`7
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`Case 1:22-cv-00311-WCB Document 414 Filed 03/22/24 Page 8 of 28 PageID #: 25202
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`correspond with the claims, because all of the depicted plasmids lack a sequence encoding the
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`Mxr1 protein.8
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`1. Sequence encoding a heme-containing protein
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`Consistent with Impossible’s construction, Figure 2(ii) of the ’492 patent (below) depicts
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`exactly what is described in the first part of claim 1 of the ’492 patent. As stated above, that part
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`of claim 1 recites “a nucleic acid molecule encoding [1] a heme-containing protein operably linked
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`to [2] a promoter element from P. pastoris and [3] a Mxr1 transcriptional activator sequence. . . .”
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`Figure 2(ii) shows exactly that. LegH, shorthand for Leghemoglobin, is a heme-containing
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`protein. And, as explained above, the promoter element and Mxr1 transcriptional activator
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`sequence are both found in the AOX1 promoter. Claim 2, which depends from claim 1, specifies
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`that “the heme-containing protein is Leghemoglobin,” as in Figure 2(ii). And claim 6, which also
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`depends from claim 1, specifies that the nucleic acid molecule further includes “a promoter
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`element from a transcriptional elongation factor EF-1 (TEF1) gene.” The promoter element of
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`claim 6 is labeled in Figure 2(ii) as the Ag TEF promoter. The sole portion of Figure 2(ii) that is
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`unaccounted for by the claims is the section labeled AmpR, which refers to a gene conferring
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`resistance to ampicillin, a common antibiotic. See ’492 patent at 22:63–65 (discussing plating
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`colonies containing the plasmids of Figure 2 on agar plates with ampicillin to eliminate cells not
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`containing the plasmid).
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`8 Figure 4 shows a plasmid with a sequence encoding the Mxr1 protein, but one would
`expect it to contain two such sequences. See infra at 13.
`8
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`Case 1:22-cv-00311-WCB Document 414 Filed 03/22/24 Page 9 of 28 PageID #: 25203
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`[1] Heme
`containing protein
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`[2] Promoter element
`from P. pastoris,
`which contains
`[3] an Mxr1 binding
`site
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`If Ginkgo and Motif’s construction were correct, the corresponding embodiment would
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`also contain a sequence encoding the Mxr1 protein linked to a separate promoter. An annotated
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`version of Figure 2(ii) embodying the first part of claim 1 under Ginkgo and Motif’s construction
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`is shown below: 9
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`9 None of the annotated figures are to scale. All of the plasmids would be much larger if
`they were to embody Ginkgo and Motif’s construction because they would contain an additional
`Mxr1 gene. The DNA sequence encoding Mxr1 alone is almost 3500 base pairs. See ’492 patent
`at 29:1–30:55. In order to show modifications on the same background image, the modified genes
`are depicted as shorter than they would be in reality.
`Annotations adding new components to the plasmids are shown in red. Annotations
`moving existing components on the plasmids to make space for new material are shown in black.
`9
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`Case 1:22-cv-00311-WCB Document 414 Filed 03/22/24 Page 10 of 28 PageID #: 25204
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`No such embodiment is present in either of the asserted patents.
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`2. Sequence encoding a protein involved in heme biosynthesis
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`Figures 2(i), (iii), (iv), and (v) of the ’492 patent all depict embodiments of the second
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`nucleic acid molecule described in claim 1. That molecule contains “a nucleic acid molecule
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`encoding [1] at least one polypeptide involved in heme biosynthesis . . . [2] a promoter element
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`from P. pastoris and [3] a Mxr1 transcriptional activator sequence . . . .” Figure 2(i) (below) is
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`representative and contains all three sequences called for by the claim under Impossible’s
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`construction. ALA dehydratase is a polypeptide involved in heme biosynthesis. See e.g., ’492
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`10
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`Case 1:22-cv-00311-WCB Document 414 Filed 03/22/24 Page 11 of 28 PageID #: 25205
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`patent at cl. 4 (“[T]he at least one polypeptide involved in heme biosynthesis is selected from the
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`group consisting of ALA synthase, ALA dehydratase . . . .”). As noted, under Impossible’s
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`construction, the AOX1 promoter contains both a promoter element and a Mxr1 transcriptional
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`activator sequence. Figures 2(iii), (iv), and (v) show plasmids encoding different combinations of
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`proteins involved in heme synthesis.. The nucleic acid encoding an Mxr1 protein, which is
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`required by Ginkgo and Motif’s constructions, is not present in any of Figures 2(i), (iii), (iv), or
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`(v).
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`[1] Protein
`involved in heme
`biosynthesis
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`[2] Promoter element from
`P. pastoris, which contains
`[3] an Mxr1 binding site
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`
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`As in the case of the heme-containing protein, the corresponding embodiment of the
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`portion of claim 1 that is directed to a protein involved in heme biosynthesis would also differ
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`from the one described in the patent following Ginkgo and Motif’s construction. In addition to
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`everything found in Figure 2(i), the corresponding embodiment under Ginkgo and Motif’s
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`
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`11
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`

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`Case 1:22-cv-00311-WCB Document 414 Filed 03/22/24 Page 12 of 28 PageID #: 25206
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`construction would also contain a sequence encoding the Mxr1 protein linked to a separate
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`promoter. An annotated version of Figure 2(i) embodying the second part of claim 1 under Ginkgo
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`and Motif’s construction is shown below:
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`
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`No such embodiment can be found in either asserted patent.
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`3. Sequence encoding the Mxr1 protein
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`Figure 4 of the ’492 patent (below) depicts an embodiment of the additional nucleic acid
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`molecule described in dependent claim 14. The additional nucleic acid molecule of claim 14
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`contains “a nucleic acid molecule encoding [1] a Mxr1 transcriptional activator . . . [2] a promoter
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`element from P. pastoris and [3] a Mxr1 transcriptional activator sequence from P. pastoris.” The
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`“nucleic acid molecule encoding a Mxr1 transcriptional activator” is the large portion labeled
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`12
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`

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`Case 1:22-cv-00311-WCB Document 414 Filed 03/22/24 Page 13 of 28 PageID #: 25207
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`Mxr1. And the promoter element and Mxr1 transcriptional activator sequences are found in the
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`AOX1 promoter.
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`[1] Mxr1 protein
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`[2] Promoter element
`from P. pastoris,
`which contains
`[3] an Mxr1 binding
`site
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`
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`At the claim construction hearing, counsel for Ginkgo argued that Figure 4 supports
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`Ginkgo’s construction because it shows a plasmid containing the Mxr1 gene, i.e., a sequence
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`encoding the Mxr1 protein. But if Figure 4 were to embody any of the claims under Ginkgo and
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`Motif’s construction, it would need to contain both the Mxr1 gene and a second gene encoding a
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`heme-containing protein (claim 1), protein involved in heme biosynthesis (claim 1), or a second
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`Mxr1 protein (claim 14). Thus, it is clear that Figure 4 is an embodiment of claim 14 under
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`Impossible’s construction, but does not embody any claims under Motif and Ginkgo’s
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`construction. A version of Figure 4 that has been annotated to embody claim 14 under Ginkgo
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`and Motif’s construction is shown below:
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`
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`13
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`

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`Case 1:22-cv-00311-WCB Document 414 Filed 03/22/24 Page 14 of 28 PageID #: 25208
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`
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`As in the case of the other claimed elements, there is no embodiment following Ginkgo and Motif’s
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`construction of claim 14 in either of the asserted patents.
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`In sum, under Impossible’s proposed construction, every nucleic acid molecule called for
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`by the claims can be found in the embodiments described in the specification. By contrast, nothing
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`in either of the asserted patents embodies the ’492 claims under Ginkgo and Motif’s construction.
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`I decline to adopt Motif and Ginkgo’s construction because it would result in the claims being
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`directed to something other than what Impossible invented. The intrinsic record makes clear that
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`Impossible’s construction is correct and that Motif and Ginkgo’s is not. See Phillips, 415 F.3d at
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`1315.
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`
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`14
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`B. Context of Use
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`In addition to aligning closely with the specification, Impossible’s construction also makes
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`more sense in context than Ginkgo and Motif’s. Context therefore provides a second reason
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`supporting Impossible’s position. See Phillips, 415 F.3d at 1314 (explaining that “the context in
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`which a term is used in the asserted claim” is often “highly instructive” in determining the correct
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`construction). As explained above, claim 14 of the ’492 patent depends from claim 1 and recites:
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` 14. The yeast cell of claim 1, further comprising a nucleic acid molecule encoding a Mxr1
`transcriptional activator operably linked to a promoter element from P. pastoris and a Mxr1
`transcriptional activator sequence from P. pastoris.
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`Claim 14 refers separately to “a nucleic acid molecule encoding a Mxr1 transcriptional
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`
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`activator” and “a Mxr1 transcriptional activator sequence.” The structure of claim 14 therefore
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`indicates that those components are two different things. “A nucleic acid encoding a Mxr1
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`transcriptional activator” unambiguously refers to the nucleic acid encoding the Mxr1 protein. As
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`such, “a Mxr1 transcriptional activator sequence” must refer to something else. And the only other
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`thing to which it could reasonably refer is the DNA sequence to which Mxr1 binds, which is what
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`Impossible’s construction dictates.
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`Ginkgo and Motif argue that the difference between the “Mxr1 transcriptional activator”
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`and the “Mxr1 transcriptional activator sequence” is that the first must be “from P. pastoris,”
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`whereas the second refers to Mxr1 from any organism. That reading of claim 14 is unnatural. If
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`that were the intended meaning of the claim language, one would expect the claim to refer to a
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`“second” Mxr1 transcriptional activator, but it does not. As such, the structure of claim 14 favors
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`Impossible’s construction.
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`Impossible’s construction is further supported by the patent’s definition of the term
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`“operably linked,” which the patent uses to mean “positioned relative to a nucleic acid coding
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`
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`15
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`

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`Case 1:22-cv-00311-WCB Document 414 Filed 03/22/24 Page 16 of 28 PageID #: 25210
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`sequence in such a way as to direct or regulate expression of the nucleic acid.” ’492 patent at
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`4:49–51; Dkt. No. 354 at ¶ 33, 42. A DNA sequence encoding the Mxr1 protein itself (Ginkgo
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`and Motif’s construction) would have nothing to do with directing or regulating the expression of
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`“a heme-containing protein” or a “polypeptide involved in heme biosynthesis.” A DNA sequence
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`to which the Mxr1 protein binds (Impossible’s construction), on the other hand, would regulate
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`transcription by binding the Mxr1 transcriptional activator. Thus, only under Impossible’s
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`construction would the Mxr1 sequence be “operably linked” to a coding region. As such,
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`Impossible’s construction makes more sense in the context in which the term is used than the
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`construction proposed by Motif and Ginkgo. Context therefore further supports Impossible’s
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`construction.
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`C. Ginkgo and Motif’s Arguments
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`Ginkgo and Motif raise two points in support of their proposed construction. The first is
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`that another patent in the same family uses “Mxr1 transcriptional activator sequence” to mean the
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`DNA sequence encoding the protein, suggesting that it should be given the same meaning in the
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`’492 patent. The second is that the Patent Trial and Appeal Board adopted Ginkgo and Motif’s
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`construction in its decision declining to institute review of the ’492 patent. Both are reasonable
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`arguments, but they are ultimately insufficient to overcome the evidence in Impossible’s favor.
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`U.S. Patent No. 9,938,327 (“the ’327 patent”) claims priority to PCT/US2016031797, the
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`same application as the ’492 and ’656 patents. The ’327 patent also uses the phrase “Mxr1
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`transcriptional activator sequence,” by which it means the DNA sequence encoding the Mxr1
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`protein. That meaning is unambiguous because dependent claim 17 further calls for an Mxr1
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`transcriptional activator sequence, wherein the sequence is a specific DNA sequence encoding the
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`16
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`Case 1:22-cv-00311-WCB Document 414 Filed 03/22/24 Page 17 of 28 PageID #: 25211
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`Mxr1 protein. Thus, the ’327 patent follows Motif and Ginkgo’s construction.10 It is well
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`established that, “unless otherwise compelled, the same claim term in the same patent or related
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`patents carries the same construed meaning.” In re Rambus Inc., 694 F.3d 42, 48 (Fed. Cir. 2012)
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`(cleaned up) (quoting Omega Eng'g, Inc. v. Raytek Corp., 334 F.3d 1314, 1334 (Fed. Cir. 2003)).
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`Here, however, the meaning of “Mxr1 transcriptional activator sequence” is “otherwise
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`compelled” by the figures and claims of the ’492 patent itself, which make clear that Impossible’s
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`construction is the correct one. Although the meaning of the term “Mxr1 transcriptional activator
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`sequence” in the ’327 patent is a point in Motif and Ginkgo’s favor, the usage of the term in the
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`’327 patent does not overcome the intrinsic evidence in the ’492 patent itself, which confirms
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`Impossible’s construction.
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`The second of Ginkgo and Motif’s points is that the Patent Trial and Appeal Boardadopted
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`their construction. See Dkt. No. 333-8, Ex. 8 at 13 (declining to institute inter partes review in
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`part because “[p]etitioner has not sufficiently shown that a POSITA . . . would have been motivated
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`to incorporate the nucleic acid sequence encoding a Mxr1 transcriptional activator”; referring to
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`the disputed term as used in claim 1 of the ’492 patent). But Ginkgo and Motif do not make a
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`collateral estoppel argument, and this court is not bound by the Board’s interpretation if it believes
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`10 Impossible argues that the term’s usage in the ’327 patent is the product of a drafting
`error, because claim 18 of the patent requires that the same term have “the amino acid sequence
`shown in [a specific identified sequence].” Claim 1 of the ’327 patent, from which claim 18
`depends, recites a “nucleic acid molecule” comprising “a Mxr1 transcriptional activator sequence.”
`According to Impossible, this discrepancy shows that the ’327 patent’s use of “a Mxr1
`transcriptional activator sequence” must be a drafting error because a nucleic acid molecule cannot
`include an amino acid sequence as contemplated by claim 18. That argument is unpersuasive for
`two reasons. First, a person of ordinary skill in the art, recognizing the mismatch between claims
`1 and 18, would understand that claim 18 requires the DNA sequence that encodes the specified
`amino acid sequence, rather than the sequence that “has” it. Second, claims 17 and 18 of the ’327
`patent both unambiguously call for sequences, whether nucleic acid or amino acid, encoding the
`Mxr1 protein, which is the crux of the immediate dispute. Errors aside, the ’327 patent clearly
`uses the disputed term in the way Ginkgo and Motif propose that it be construed.
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`Case 1:22-cv-00311-WCB Document 414 Filed 03/22/24 Page 18 of 28 PageID #: 25212
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`that interpretation to be incorrect. I am not persuaded that the construction of the term adopted by
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`the Patent Trial and Appeal Board is correct.
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`For the foregoing reasons, the court construes “a Mxr1 transcriptional activator sequence”
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`to mean “a DNA sequence to which the Mxr1 transcriptional activator protein binds.”
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`Term 2b: “a first exogenous nucleic acid encoding a methanol expression regulator 1
`(Mxr1) transcriptional activator”
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`The parties do not dispute that Term 2b refers to the sequence encoding the Mxr1
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`transcriptional activator protein. Dkt. No. 371 at 9. For consistency with the other terms, see infra
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`Term 2c, I construe this term to mean “a first exogenous nucleic acid encoding a methanol
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`expression regulator 1 (Mxr1) transcriptional activator protein.”
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`Term 2c: “a nucleic acid encoding a Mxr1 transcriptional activator sequence”
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`The parties do not dispute that Term 2c refers to the sequence encoding the Mxr1
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`transcriptional activator protein. Dkt. No. 371 at 9. The word “sequence” is not specific, however,
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`in that it can refer to the sequence to which Mxr1 binds or to the sequence encoding the Mxr1
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`protein. For clarity and consistency, I construe this term to mean “a nucleic acid encoding a Mxr1
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`transcriptional activator protein.”
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`Term 3: “from P. pastoris” or “from Pichia pastoris”
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`The parties propose conflicting constructions of what it means to be “from P. pastoris.”
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`Impossible proposes that “from P. pastoris” “indicates that the sequence has its origins in the P.
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`pastoris genome.” Ginkgo and Motif’s proposed constructions require that the thing be found in
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`native P. pastoris, i.e., found naturally in P. pastoris. The main difference between the parties’
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`constructions relates to whether “from P. pastoris” includes sequences that originated in the P.
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`pastoris genome but have subsequently been modified. Impossible’s construction would
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`18
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`Case 1:22-cv-00311-WCB Document 414 Filed 03/22/24 Page 19 of 28 PageID #: 25213
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`encompass some such sequences; Ginkgo and Motif’s would not. For the reasons set forth below,
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`I adopt Impossible’s proposed construction.
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`As an initial matter, Impossible argues that Motif’s use of the term “native” contradicts the
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`specification. The parties, however, appear to be speaking past one another on this issue. Synthetic
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`biology, the field of the patents