Case 1:22-cv-00311-WCB Document 338 Filed 01/26/24 Page 1 of 27 PageID #: 20815
`
`IN THE UNITED STATES DISTRICT COURT
`FOR THE DISTRICT OF DELAWARE
`
`C.A. No. 22-311-WCB
`
`JURY TRIAL DEMANDED
`
`))))))))))
`
`IMPOSSIBLE FOODS INC.,
`
`Plaintiff,
`
`v.
`
`MOTIF FOODWORKS, INC. and
`GINKGO BIOWORKS, INC.,
`
`Defendants.
`
`PLAINTIFF IMPOSSIBLE FOODS INC.’S
`ANSWERING CLAIM CONSTRUCTION BRIEF
`
`OF COUNSEL:
`
`Wendy L. Devine
`Kristina M. Hanson
`Shannon P. Gillespie McComb
`Jessica Ramsey
`Susannah M. L. Gagnon
`Joyce K. Yao
`WILSON SONSINI GOODRICH & ROSATI, P.C.
`One Market Plaza
`Spear Tower, Suite 3300
`San Francisco, CA 94105
`Tel: (415) 947-2000
`
`Matthew R. Reed
`WILSON SONSINI GOODRICH & ROSATI, P.C.
`650 Page Mill Road
`Palo Alto, CA 94304
`Tel: (650) 493-9300
`
`Lori P. Westin
`Natalie J. Morgan
`WILSON SONSINI GOODRICH & ROSATI, P.C.
`12235 El Camino Real
`San Diego, CA 92130
`Tel: (858) 350-2300
`
`Dated: January 26, 2024
`11292192 / 20200.00002
`
`David E. Moore (#3983)
`Bindu A. Palapura (#5370)
`Andrew M. Moshos (#6685)
`POTTER ANDERSON & CORROON LLP
`Hercules Plaza, 6th Floor
`1313 N. Market Street
`Wilmington, DE 19801
`Tel: (302) 984-6000
`dmoore@potteranderson.com
`bpalapura@potteranderson.com
`amoshos@potteranderson.com
`
`Attorneys for Plaintiff Impossible Foods Inc.
`
`OF COUNSEL:
`
`Michael T. Rosato
`WILSON SONSINI GOODRICH & ROSATI, P.C.
`701 Fifth Avenue
`Suite 5100
`Seattle, WA 98104
`Tel: (206) 883-2529
`
`

`

`Case 1:22-cv-00311-WCB Document 338 Filed 01/26/24 Page 2 of 27 PageID #: 20816
`
`TABLE OF CONTENTS
`
`I.
`II.
`
`III.
`
`2.
`3.
`
`B.
`
`C.
`
`D.
`
`PAGE
`Introduction ..........................................................................................................................1
`Disputed Terms ....................................................................................................................1
`A.
`Promoter Element (Ginkgo’s Numbering: Term 1; Motif’s Numbering:
`Term 26)...................................................................................................................1
`1.
`A “promoter element” is a discrete nucleic acid structure with a role in
`protein expression ....................................................................................... 2
`Promoters are not broader than promoter elements .................................... 3
`Promoter element is not a nonce word and the Asserted Claims are not
`means-plus-function claims ........................................................................ 4
`Mxr1 claim terms (Ginkgo’s Numbering: Terms 2a-c; Motif’s Numbering:
`Terms 18-20) ............................................................................................................6
`1.
`Claim 14 of the ’492 Patent Supports Impossible’s Construction .............. 7
`2.
`Ginkgo’s arguments do not support its construction .................................. 9
`Sequence to which [the/a] Mxr1 transcriptional activator binds (Ginkgo’s
`Numbering: Term 6) ..............................................................................................11
`“From P. pastoris” (Ginkgo’s Numbering: Term 3; Motif’s Numbering:
`Terms 18-20) ..........................................................................................................13
`Claims 1 and 14 of the ’492 Patent (Ginkgo’s Numbering: Term 5; Motif’s
`Numbering: Terms 18) ...........................................................................................14
`“The” promoter element (Ginkgo’s Numbering: Term 8) .....................................15
`Same nucleic acid (Ginkgo’s Numbering: Term 4) ...............................................17
`Wherein each nucleic acid is operably linked to a methanol-inducible
`promoter element (Ginkgo’s Numbering Term 7) ................................................19
`1.
`Operable linkage to promoter element ...................................................... 19
`2.
`Same Nucleic Acid ................................................................................... 21
`Conclusion .........................................................................................................................21
`
`E.
`
`F.
`G.
`H.
`
`i
`
`

`

`Case 1:22-cv-00311-WCB Document 338 Filed 01/26/24 Page 3 of 27 PageID #: 20817
`
`TABLE OF AUTHORITIES
`
`PAGE(S)
`
`CASES
`ActiveVideo Networks, Inc. v. Verizon Commc’ns, Inc.,
`694 F.3d 1312 (Fed. Cir. 2012)..........................................................................................15
`Amsted Indus., Inc. v. ABC-Naco, Inc.,
`No. 00 C 7119, 2001 WL 826904 (N.D. Ill. July 18, 2001) ..............................................16
`Baldwin Graphic Sys., Inc. v. Siebert, Inc.,
`512 F.3d 1338 (Fed. Cir. 2008)..............................................................................16, 17, 20
`Bushnell Hawthorne, LLC v. Cisco Sys., Inc.,
`813 F. App’x 522 (Fed. Cir. 2020) ....................................................................................17
`EPOS Techs. Ltd. v. Pegasus Techs. Ltd.,
`766 F.3d 1338 (Fed. Cir. 2014)..........................................................................................20
`Erfindergemeinschaft UroPep GbR v. Eli Lilly & Co.,
`No. 2:15-CV-1202-WCB, 2016 WL 6138124 (E.D. Tex. Oct. 21, 2016) ...........................5
`Fisher-Price, Inc. v. Graco Children’s Prods., Inc.,
`154 F. App’x 903 (Fed. Cir. 2005) ....................................................................................16
`Free Motion Fitness, Inc. v. Cybex Int’l, Inc.,
`423 F.3d 1343 (Fed. Cir. 2005)..........................................................................................16
`Phillips v. AWH Corp.,
`415 F.3d 1303 (Fed.Cir.2005)............................................................................................20
`S3 Inc. v. NVIDIA Corp.,
`259 F.3d 1364 (Fed. Cir. 2001)........................................................................................3, 4
`Williamson v. Citrix Online, LLC,
`792 F.3d 1339 (Fed. Cir. 2015)........................................................................................5, 6
`Zeroclick, LLC v. Apple Inc.,
`891 F.3d 1003 (Fed. Cir. 2018)..........................................................................................12
`
`ii
`
`

`

`Case 1:22-cv-00311-WCB Document 338 Filed 01/26/24 Page 4 of 27 PageID #: 20818
`
`TABLE OF ABBREVIATIONS
`
`Abbreviation
`
`Phrase
`
`Impossible
`
`Impossible Foods Inc.
`
`Ginkgo
`
`Motif
`
`’492 patent
`
`’656 patent
`
`’327 patent
`
`Ginkgo Bioworks, Inc.
`
`Motif FoodWorks, Inc.
`
`U.S. Patent No. 10,273,492
`
`U.S. Patent No. 10,689,656
`
`U.S. Patent No. 9,938,327
`
`Yeast Patents
`
`’492 and ’656 patents, collectively
`
`Ginkgo’s Numbering
`Term __
`
`Numbered list of terms in the Joint Claim Construction Statement for
`the Yeast Patents (D.I. 314-1).
`
`POSA
`
`Alper I
`
`Alper II
`
`Alper III
`
`person of ordinary skill in the art
`
`D.I. 107
`
`D.I. 144
`
`Declaration of Dr. Hal Alper filed herewith
`
`iii
`
`

`

`Case 1:22-cv-00311-WCB Document 338 Filed 01/26/24 Page 5 of 27 PageID #: 20819
`
`I.
`
`INTRODUCTION
`
`Ginkgo’s indefiniteness arguments and proposed constructions are at odds with the
`
`intrinsic record and the common knowledge of those of ordinary skill in the art. Indeed,
`
`Ginkgo’s arguments are premised on divorcing the claim terms that Ginkgo crafted (often
`
`misleadingly re-writing the claim language) from the context of the claims and the specification.
`
`Ginkgo then compounds its erroneous analysis by disregarding a POSA’s knowledge, the details
`
`of which Ginkgo’s own expert admits. Even accepting these contortions, Ginkgo fails to identify
`
`any evidence—let alone clear and convincing evidence—showing indefiniteness.
`
`II.
`
`DISPUTED TERMS
`
`A.
`
`Promoter Element (Ginkgo’s Numbering: Term 1; Motif’s Numbering:
`Term 26)
`
`Claim Term
`“promoter element”
`(all asserted claims)
`
`Ginkgo
`Indefinite
`
`Impossible
`Plain and ordinary meaning. No
`construction is necessary.
`To the extent that this term is construed:
`a polynucleotide that regulates (e.g.,
`drives) transcription of a polynucleotide
`sequence (e.g., gene)
`a promoter element is upstream of, and
`adjacent to or in close physical proximity
`to the gene
`See D.I. 94-1, 106, 142.
`
`Ginkgo failed to meet its burden of showing, by clear and convincing evidence, that a
`
`POSA would not understand the meaning of “promoter element” with reasonable certainty.
`
`Ginkgo strips “promoter element” from its context—including the claim language, the
`
`specification, and the understanding of a POSA—and asserts that promoter elements are variable
`
`and modular. That is not evidence of indefiniteness.
`
`

`

`Case 1:22-cv-00311-WCB Document 338 Filed 01/26/24 Page 6 of 27 PageID #: 20820
`
`1.
`
`A “promoter element” is a discrete nucleic acid structure with a role in
`protein expression1
`
`A “promoter element” corresponds to a specific form or structure—a nucleic acid
`
`sequence—not function alone. Alper III, ¶¶ 23-38; Alper I, ¶¶ 17-68; Alper II, ¶¶ 17-32. A
`
`POSA understands that promoter elements are discrete nucleic acid sequences (polynucleotides)
`
`that regulate transcription of a gene and are positioned upstream of and adjacent (or in
`
`proximity) to said gene. Alper III, ¶¶ 23-38; Alper I, ¶¶ 17-68; Alper II, ¶¶ 17-32. Though there
`
`are options for a POSA to truncate or expand a given promoter element, there is no uncertainty
`
`as to what, in fact, a promoter element is. A promoter element is a functional part of a
`
`promoter—not just any sequence, but rather a discrete unit with a particular identity in the
`
`scientific literature.
`
`Ginkgo’s expert, Dr. Batt, states that “element” does not indicate sequence or function,
`
`which ignores the relevant claim language, “promoter element,” and admits that promoters were
`
`well known to a POSA. Batt, ¶ 64; Alper III, ¶¶ 11-22, 25. Despite familiarity with promoters,
`
`Dr. Batt somehow contends that a POSA would not be familiar with the phrase “promoter
`
`element”—an opinion contradicted by the literature in the field and Ginkgo’s own patent
`
`applications. Alper III, ¶¶ 26-32. Various publications in the field discuss “promoter elements”
`
`including their composition, structure, function, and how POSAs make and use them. Id. Usage
`
`of the phrase “promoter element” in the Yeast Patents is consistent with that usage in the
`
`literature and with Dr. Alper’s opinions. Id., ¶ 30. Unsurprisingly, Ginkgo’s own patent
`
`1 Ginkgo mischaracterizes Impossible’s position with selective quoting from a status conference
`while ignoring Impossible and Motif’s briefing on “promoter element,” which was filed and in
`Ginkgo’s possession several months ago, and repeatedly referenced at that status conference. As
`Impossible has explained, a “promoter element” is not a means-plus-function claim limitation—
`the term is not a mere verbal construct or placeholder recitation but rather “conveys to the person
`of skill in the art a variety of structures,” based on knowledge in the field, that direct and regulate
`expression. D.I. 333-3 at 10:13-19; see also D.I. 106 at 15.
`
`-2-
`
`

`

`Case 1:22-cv-00311-WCB Document 338 Filed 01/26/24 Page 7 of 27 PageID #: 20821
`
`applications also discuss “promoter element” in manner consistent with Impossible’s proposed
`
`construction. Id., ¶ 32.
`
`Dr. Batt alleges that the Yeast Patents do not provide an express definition or working
`
`example of a promoter element. First, neither is required for definiteness, especially in view of
`
`the POSA’s familiarity with and understanding of the phrase. Id., ¶ 33; S3 Inc. v. NVIDIA Corp.,
`
`259 F.3d 1364, 1371 (Fed. Cir. 2001) (“The law is clear that patent documents need not include
`
`subject matter that is known in the field of the invention and is in the prior art, for patents are
`
`written for persons experienced in the field of the invention.”). Dr. Batt also apparently fails to
`
`realize that the Yeast Patents do contain examples of promoter elements that drive transcription
`
`of genes. 8, ¶ 33.
`
`Dr. Batt contends that the patents do not describe what makes a given nucleotide
`
`sequence a promoter element. Dr. Batt is wrong. The Yeast Patents state that promoter elements
`
`were known in the art and provide examples. Alper III, ¶¶ 34, 38. Moreover, Dr. Batt’s own
`
`admissions regarding what was known in the art contradict his opinion. Id., ¶¶ 11-22.
`
`Finally, Dr. Batt removes the phrase “promoter element” from the claims and the
`
`knowledge of the POSA entirely to opine that the number of potential promoter elements are
`
`“practically infinite” and to speculate about promoter element function in unknown contexts.
`
`The POSA has knowledge of promoter elements, their characteristics, and how to make use of
`
`them. Id., ¶¶ 36-37. Dr. Batt’s analysis finds no support in the law of definiteness.
`
`2.
`
`Promoters are not broader than promoter elements
`
`Ginkgo states that “‘therefrom’ language is used repeatedly . . . to distinguish between
`
`‘promoter elements’ and ‘promoters,’” and mistakenly concludes that the Yeast Patents’
`
`specification’s teachings of promoters are thus inapplicable to “promoter elements.” D.I. 333 at
`
`2-3. Not so. The indefiniteness analysis proceeds through the lens of a POSA, who would know
`
`-3-
`
`

`

`Case 1:22-cv-00311-WCB Document 338 Filed 01/26/24 Page 8 of 27 PageID #: 20822
`
`that promoter elements are specific structures within a promoter. S3 Inc., 259 F.3d at 1371;
`
`Alper III, ¶¶ 26-29.
`
`A POSA understands that promoter elements are discrete sequences found in larger
`
`promoter sequences. Thus, if a promoter sequence is present in a nucleic acid construct, a
`
`promoter element necessarily is present as well; a promoter element, however, may be present
`
`even when the entire promoter is not. Alper III, ¶¶ 28, 29. Accordingly, “promoter element” has
`
`a broader scope than “promoter,” not a narrower scope as Ginkgo incorrectly assumes. The
`
`claims of U.S. Patent No. 9,938,327 (“the ’327 patent”), support this understanding.2 Claim 11
`
`of the ’327 patent recites a yeast cell “wherein the AOX1 promoter element has the nucleic acid
`
`sequence shown in SEQ ID NO:7,” and the specification states that SEQ ID NO:7 is the full
`
`sequence of the Pichia pastoris pAOX1 promoter. D.I. 333-5 at claim 11, 33:5-20. Ginkgo’s
`
`own patent applications likewise reflect the greater breadth of “promoter element” relative to
`
`“promoter.” Alper III, ¶ 32.
`
`3.
`
`Promoter element is not a nonce word and the Asserted Claims are not
`means-plus-function claims
`
`Ginkgo’s means-plus-function argument entirely fails to address any of Impossible’s
`
`prior briefing on the issue. D.I. 333 at 3-4 (failing to address Impossible’s arguments at D.I. 142
`
`at 15-16).
`
`Ginkgo relies on a false dichotomy between “what [something] does” and “what
`
`[something] is” and incorrectly argues that “promoter element” refers to function alone. D.I. 333
`
`at 4 (emphasis in original). A “promoter element” has a purpose or function in addition to a
`
`structure, as explained above and in Impossible’s previous briefing. D.I. 142 at 15-16.
`
`2 Ginkgo raised the ’327 patent in its brief. The ’327 patent is not asserted in this case, but it is
`related to the asserted Yeast Patents.
`
`-4-
`
`

`

`Case 1:22-cv-00311-WCB Document 338 Filed 01/26/24 Page 9 of 27 PageID #: 20823
`
`Acknowledging that a promoter element serves a function in protein expression (the objective of
`
`the Asserted Patents) in no way supports Ginkgo’s conclusion that a POSA would not know
`
`“what [a promoter element] is.” See Erfindergemeinschaft UroPep GbR v. Eli Lilly & Co., No.
`
`2:15-CV-1202-WCB, 2016 WL 6138124, at *9 (E.D. Tex. Oct. 21, 2016) (“In construing claims
`
`in light of section 112 paragraph 6, it is important to confine that statutory provision to cases for
`
`which it was designed to apply, and not to apply it mechanically whenever any seemingly
`
`functional term appears anywhere in a claim. That provision allows drafters to describe a
`
`structure, material, or act by its function, with the understanding that the structure, material, or
`
`act will be limited by what is disclosed in the specification. Drafters should not, however, be
`
`confined by section 112 paragraph 6 when they use a term that is understood by persons of skill
`
`in the art to have a meaning that denotes structure, even though the term may also describe the
`
`function performed by the object in question. Instead, in such cases the conventional tools of
`
`claim construction should be applied to discern the scope of the term.”).
`
`Ginkgo’s position is based on a misapprehension of “element” and a failure to consider
`
`the term from a POSA’s perspective. D.I. 333 at 3. Ginkgo’s only cited case has no
`
`applicability to “promoter element” or to the Yeast Patent claims. Id. at 4 (citing Williamson v.
`
`Citrix Online, LLC, 792 F.3d 1339, 1352 (Fed. Cir. 2015)). Williamson discusses the claim term
`
`“module” in a patent directed to “methods and systems for ‘distributed learning’ that utilize
`
`industry standard computer hardware and software” to provide a virtual classroom. The Yeast
`
`Patent claims at issue here do not relate to hardware and software methods and systems but
`
`rather encompass specific nucleic acid molecules used for recombinant protein expression. A
`
`promoter “element” in the field of the present invention has a different meaning from “element”
`
`-5-
`
`

`

`Case 1:22-cv-00311-WCB Document 338 Filed 01/26/24 Page 10 of 27 PageID #: 20824
`
`in Citrix and refers to specific nucleic acid structures with physical loci, the structures of which
`
`are known to the POSA. Alper III, ¶¶ 23-38.
`
`B.
`
`Mxr1 claim terms (Ginkgo’s Numbering: Terms 2a-c; Motif’s Numbering:
`Terms 18-20)
`
`Ginkgo
`a sequence of an Mxr1
`transcriptional activator
`protein
`
`Impossible
`Plain and ordinary meaning,
`which is the sequence to which
`the Mxr1 transcriptional
`activator protein binds
`See D.I. 94-1,106, 142.
`Plain and ordinary meaning,
`which is the nucleic acid
`encoding the Mxr1
`transcriptional activator protein
`See D.I. 94-1,106, 142.
`
`Claim Term
`a Mxr1 transcriptional
`activator sequence from P.
`pastoris
`’492 patent, cls. 1, 14
`
`a first exogenous nucleic acid
`encoding a methanol
`expression regulator 1 (Mxr1)
`transcriptional activator3
`’656 patent, cl. 1
`a nucleic acid encoding a Mxr1
`transcriptional activator
`sequence from P. pastoris
`’656 patent, cl. 26
`
`Ginkgo abbreviates this claim language to strip it of important context within the
`
`claims—including the express claim language “operably linked” and “a nucleic acid
`
`encoding”—and thereby distort its meaning. Only by narrowing the field of view to remove
`
`context and failing to engage with the logic of Impossible’s prior briefing, (D.I. 106, Alper I, 142,
`
`Alper II), is Ginkgo able to perceive the language of the ’492 patent claims as “nearly identical” or
`
`“identical” to the language of the ’656 patent claims. D.I. 333 at 8. This is plainly false. Terms 2b
`
`and 2c are found in the ’656 patent claims following important contextual language—“a nucleic
`
`3 Ginkgo re-numbers this phrase as “2b” and shortens it to remove “a first exogenous nucleic
`acid encoding” without explanation. Impossible has recited the term as it appears in prior
`briefing as Term 19.
`
`-6-
`
`

`

`Case 1:22-cv-00311-WCB Document 338 Filed 01/26/24 Page 11 of 27 PageID #: 20825
`
`acid encoding.” In contrast, Term 2a is found in the ’492 patent claims following different
`
`context—“operably linked to a promoter element from P. pastoris and…”.
`
`1.
`
`Claim 14 of the ’492 Patent Supports Impossible’s Construction
`
`The ’492 patent makes clear that Term 2a is not identical to Terms 2b and 2c. A
`
`comparison of ’492 patent claims 1 and 14 with claim limitations organized into expression
`
`“modules” labeled [a], [b], and [c]:
`
`’492 patent
`Claims 1 and 14
`1. A methylotrophic Pichia yeast cell
`comprising:
`[a] 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
`[b] 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.
`
`14. The yeast cell of claim 1, further
`comprising
`[c] a nucleic acid molecule encoding
`a Mxr1 transcriptional activator
`operably linked to
`a promoter element from P.
`pastoris and
`
`Plain and ordinary
`meaning
`
`Ginkgo’s
`construction
`
`a consensus sequence
`to which the Mxr1
`transcriptional
`activator protein binds
`
`a sequence of an Mxr1
`transcriptional
`activator protein
`
`a consensus sequence
`to which the Mxr1
`transcriptional
`activator protein binds
`
`a sequence of an Mxr1
`transcriptional
`activator protein
`
`sequence encoding
`Mxr1 transcriptional
`activator protein
`
`a sequence of an Mxr1
`transcriptional
`activator protein
`
`-7-
`
`

`

`Case 1:22-cv-00311-WCB Document 338 Filed 01/26/24 Page 12 of 27 PageID #: 20826
`
`a Mxr1 transcriptional activator
`sequence from P. pastoris.
`
`a consensus sequence
`to which the Mxr1
`transcriptional
`activator protein binds
`
`a sequence of an Mxr1
`transcriptional
`activator protein
`
`Independent claim 1 recites nucleic acid molecules [a] and [b]. Each of [a] and [b] couples
`
`a sequence encoding a protein (either a “heme-containing protein” or “at least one polypeptide
`
`involved in heme biosynthesis”) to two components: a promoter element from P. pastoris and “a
`
`Mxr1 transcriptional activator sequence [Term 2a].” Being “operably linked” to those two
`
`components allows transcription of [a] and [b]—transcription machinery can bind promoter
`
`elements, and transcriptional activator Mxr1 can bind its consensus sequence and “activate” the
`
`process. Ginkgo’s construction would mean that claim 1 instead recites a protein-encoding
`
`sequence (operably linked to a promoter element) and another protein-encoding sequence (i.e., a
`
`sequence encoding an Mxr1 transcriptional activator protein) that is not operably linked to
`
`anything. Notably, Impossible’s construction tracks the stipulated construction (and express
`
`definition in the specification) of “operably linked;” Ginkgo’s does not.
`
`Dependent claim 14 further requires a nucleic acid molecule encoding a Mxr1
`
`transcriptional activator [c], which, like [a] and [b] of claim 1, is operably linked to a promoter
`
`element and “a Mxr1 transcriptional activator sequence from P. pastoris.” The entire paradigm of
`
`claim 1 is to link a protein-encoding sequence to a promoter element and an Mxr1 consensus
`
`binding sequence (i.e., an expression element, specifically an enhancer sequence). D.I. 333-1
`
`(’656 patent) at 10:3-5 (“Expression elements can include… enhancer sequences.”). Dependent
`
`claim 14 follows this paradigm under Impossible’s construction, where the protein-encoding
`
`sequence corresponds to Mxr1, which also is linked to a promoter element and a Mxr1
`
`transcriptional activator sequence. Ginkgo’s proposed meaning “would duplicate the phrase ‘a
`
`-8-
`
`

`

`Case 1:22-cv-00311-WCB Document 338 Filed 01/26/24 Page 13 of 27 PageID #: 20827
`
`nucleic acid molecule encoding a Mxr1 transcriptional activator’ while erasing the requirement for
`
`an Mxr1 target sequence” resulting in inconsistencies in claim language. Alper I, ¶ 55.
`
`2.
`
`Ginkgo’s arguments do not support its construction
`
`Ginkgo’s citation to the specification’s disclosure of the gene encoding a Mxr1
`
`transcriptional activator sequence fails to consider the different context in which “a Mxr1
`
`transcriptional activator sequence” appears. D.I. 333 at 6. Both the specification and the ’492
`
`claims make clear that the surrounding language matters.
`
`Ginkgo’s citation to the PTAB’s denial of Motif’s IPR petition for the ’492 patent is
`
`equally unconvincing. Id. First, the PTAB did not engage in any claim construction in denying
`
`institution. D.I. 335–58 at 7. Second, the PTAB statement cited by Ginkgo is a statement rejecting
`
`the positions presented by Motif. Id. at 11 (“Petitioner’s arguments are not persuasive. Petitioner
`
`has not sufficiently shown why a POSITA would have been motivated to produce a nucleic acid
`
`that encodes both . . . .”) (emphasis added). That Motif presented arguments based on a flawed
`
`reading of the claims and the PTAB rejected them is not support for Ginkgo’s incorrect
`
`construction.
`
`Ginkgo’s suggestion that “nothing in the specification suggests that Term 2a refers to a
`
`binding site for Mxr1” ignores the actual teachings of the Yeast Patents. The patents are directed
`
`to the expression of protein in genetically engineered yeast. E.g., D.I. 333-1 at (54), 1:38-49,
`
`3:44-46. A POSA understands that to accomplish such expression requires expression elements
`
`(e.g., promoter elements and binding sites for transcriptional activators). The specification
`
`discusses nucleic acids encoding a protein to be expressed that is “operably linked” to a promoter
`
`or other expression element, and defines that relationship: “[a]s used herein, ‘operably linked’
`
`means that a promoter or other expression element(s) are positioned relative to a nucleic acid
`
`coding sequence in such a way as to direct or regulate expression of the nucleic acid (e.g., in-
`
`-9-
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`Case 1:22-cv-00311-WCB Document 338 Filed 01/26/24 Page 14 of 27 PageID #: 20828
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`frame).” Id. at 4:47-51.4 Ginkgo’s Term 2 in the ’492 patent is part of a larger phrase discussing
`
`a nucleic acid encoding a protein that is operably linked to a promoter element and [Term 2].
`
`That language and the specification’s discussion of operable linkage shows that Term 2a refers to
`
`a binding site for Mxr1. Alper III, ¶ 42-43.
`
`Ginkgo’s incorrect contention that the specification must explicitly list sequences for
`
`Mxr1 binding sites also does not support its construction. D.I. 333 at 6. As Impossible stated in
`
`its interrogatory response, as Ginkgo’s expert admits, and as discussed below, a POSA would
`
`have been aware of the sequences bound by the Mxr1 transcriptional activator. D.I. 333-4 at 19
`
`(Response to Interrogatory No. 16); infra, § II. C; Alper III, ¶¶ 40-41.
`
`Likewise, that the claims of the ’656 patent use different language to recite the Mxr1
`
`binding site does not support Ginkgo’s argument. D.I. 333 at 7. The structure and context of the
`
`claims of the ’492 and ’656 patent claims are different, and that is reflected in their phrasing.
`
`Notably, Ginkgo does not cite any case law supporting the notion that related patents must
`
`employ identical claim phrasing, because there is none.
`
`Finally, Ginkgo’s citation to a drafting error in dependent claim 17 of the ’327 patent (a
`
`patent that is not at issue in this case) also fails to support its construction. Id. The error in claim
`
`17 is also found in claim 18, which specifies that the “Mxr1 transcriptional activator sequence” is
`
`the “Mxr1 protein sequence.” D.I. 333-5 at claim 18 (“has the amino acid sequence shown in
`
`SEQ ID No: 2”), column 29 (defining SEQ ID No: 2 as “Mxr1 protein sequence”). The “Mxr1
`
`transcriptional activator sequence” of claim 1 cannot be an amino acid sequence as recited in
`
`claim 18 because claim 1 encompasses “a nucleic acid molecule.” Likewise, the “Mxr1
`
`4 The parties stipulated to this construction of “operably linked.” D.I. 314-1 at 1.
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`-10-
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`Case 1:22-cv-00311-WCB Document 338 Filed 01/26/24 Page 15 of 27 PageID #: 20829
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`transcriptional activator sequence” of claim 1 cannot be the gene encoding Mxr1, because what
`
`is recited is an Mxr1 binding site.
`
`C.
`
`Sequence to which [the/a] Mxr1 transcriptional activator binds (Ginkgo’s
`Numbering: Term 6)
`
`Claim Term
`sequence to which [the/a]
`Mxr1 transcriptional activator
`binds
`’656 patent, 1, 26
`
`Impossible
`Plain and ordinary meaning
`See D.I. 94-1, 106, 142.
`
`Ginkgo
`
`Indefinite
`
`Ginkgo’s indefiniteness contention regarding this claim phrase is supported only by the
`
`incorrect contention that the specification must explicitly list sequences for Mxr1 binding sites.
`
`D.I. 333 at 6. As discussed above with respect to Ginkgo’s Term 2, and as Ginkgo’s expert
`
`admits, a POSA would have been aware of the sequences bound by the Mxr1 transcriptional
`
`activator. D.I. 333-4 at 19 (Response to Interrogatory No. 16); Alper III, ¶¶ 44-53.
`
`As both sides’ experts acknowledge, the Mxr1 consensus sequences were known in the
`
`literature well before the priority date of the Yeast Patents. Alper III, ¶¶ 46, 48; Batt, ¶ 126. For
`
`example, a 2010 publication authored by Kranthi et al. discusses sequences that bind Mxr1 (i.e.,
`
`consensus sequences) and demonstrates that Mxr1 consistently binds its consensus sequences.
`
`Alper III, ¶ 48. Another Motif expert that filed a declaration in support of Motif’s failed IPR
`
`petitions also acknowledged this fact. Ex. 9 at ¶ 74 (Lin-Cereghino Declaration) (“Mxr1p binds
`
`to and activates various promoter sequences—for example, the promoters associated with the
`
`genes dihydroxyacetone synthase (DHAS) and peroxin 8 (PEX8). EX-1023 (Kranthi (2010)),
`
`Abstract, 710-11 (reporting “new insights into the molecular determinants of target gene
`
`specificity of Mxr1p” based on promoter mapping, in particular that Mxr1p preferably binds to
`
`DNA sequences containing the CYCCNY motif).”). Given these facts, Ginkgo cannot meet its
`
`-11-
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`Case 1:22-cv-00311-WCB Document 338 Filed 01/26/24 Page 16 of 27 PageID #: 20830
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`burden of demonstrating that a POSA does not understand this claim term with reasonable
`
`certainty.
`
`Perhaps recognizing this, Ginkgo’s expert discusses the notion of a sequence which Mxr1
`
`binds in the abstract, entirely removed from the context of the asserted claims of the Yeast
`
`Patents, and claims that there are lots of Mxr1 binding sites in the genome of P. pastoris. Batt,
`
`¶¶ 125, 129-131. This too fails to support Ginkgo’s argument as breadth is not indefiniteness.
`
`But, regardless, isolated Mxr1 binding sites in the genome of P. pastoris are not the context of
`
`this claim language—this language is found in claims requiring, inter alia, a recited promoter
`
`element and operable linkage to a specified nucleic acid. Alper III, ¶¶ 46, 49-51. Similarly,
`
`Ginkgo’s expert discusses mutation impacts on promoter strength, but fails to explain how that
`
`supports a conclusion that a POSA would not understand what an Mxr1 binding site is with
`
`reasonable certainty. Batt, ¶ 131; Alper III, ¶ 52.
`
`Ginkgo also failed to meet its burden of rebutting the presumption that this claim
`
`language, which does not recite the word “means,” has definite structure. Zeroclick, LLC v.
`
`Apple Inc., 891 F.3d 1003, 1008 (Fed. Cir. 2018). The claim, read by a POSA in view of the
`
`POSA’s knowledge, recites a nucleic acid structure. Again, as with “promoter element,” Ginkgo
`
`fails to consider this claim language in context and from the perspective of a POSA and fails to
`
`cite any applicable case law. Supra.
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`-12-
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`Case 1:22-cv-00311-WCB Document 338 Filed 01/26/24 Page 17 of 27 PageID #: 20831
`
`D.
`
`“From P. pastoris” (Ginkgo’s Numbering: Term 3; Motif’s Numbering:
`Terms 18-20)5
`
`Claim Term
`“[x] from P. pastoris / [x] from
`Pichia pastoris”
`’492 patent, cls. 1, 5, 7, and 14
`’656 patent, cls. 7, 10, 11, 26,
`28
`
`Impossible6
`Plain and ordinary meaning
`See D.I. 94-1, 106, 142.
`
`Ginkgo
`x found naturally in P. pastoris
`Motif’s construction substitutes
`“native” for “naturally”
`See D.I. 94-1, 120, 148.
`
`Again, Ginkgo fails to address any of the prior briefing on this issue despite being in
`
`possession of that briefing for 6 months. D.I. 106 at 14-15; Alper 1, ¶¶ 57-62; 142 at 10-12;
`
`Alper II, ¶¶ 11-16; 120 at 23-25; 148 at 7-8. Further, despite not adopting Motif’s construction,
`
`and instead advocating a different variation, Ginkgo also does not address Motif’s construction
`
`or Motif’s briefing at all. To date, although Impossible has asked, neither Ginkgo nor Motif
`
`have explained how, if at all, their constructions are different. D.I. 333-3 at 13:2-12. To the
`
`extent that Ginkgo is advocating for an equivalent construction to the one Motif proposed in
`
`prior briefing, Impossible opposes for the same reasons discussed in Impossible’s briefing. For
`
`example, to the extent that Ginkgo contends that this claim language is limited to a “native” or
`
`“wildtype” or “endogenous” sequence (as Motif contended in prior briefing), th