Case 1:22-cv-00311-WCB Document 345 Filed 02/02/24 Page 1 of 37 PageID #: 22395
`
`IN THE UNITED STATES DISTRICT COURT
`FOR THE DISTRICT OF DELAWARE
`
`IMPOSSIBLE FOODS INC.,
`
`Plaintiff,
`
`v.
`
`MOTIF FOODWORKS, INC., and
`GINKGO BIOWORKS, INC.,
`
`Defendants.
`
`)
`)
`)
`)
`)
`)
`)
`)
`)
`)
`)
`
`Civil Action No. 22-311-WCB
`
`JURY TRIAL DEMANDED
`
`DECLARATION OF DR. GEOFFREY LIN-CEREGHINO
`IN SUPPORT OF MOTIF’S ANSWERING CLAIM CONSTRUCTION BRIEF
`
`PUBLIC VERSION
`
`Confidential Version Filed: January 26, 2024
`
`Public Version Filed: February 2, 2024
`
`

`

`Case 1:22-cv-00311-WCB Document 345 Filed 02/02/24 Page 2 of 37 PageID #: 22396
`
`Table of Contents
`
`
`I.
`
`Introduction................................................................................................................................... 3
`
`II. Qualifications and Expertise ........................................................................................................ 3
`
`III.
`
`IV.
`
`Scope of Assignment ................................................................................................................ 6
`
`Summary of Opinions ............................................................................................................... 8
`
`V. Legal Understanding .................................................................................................................... 9
`
`A.
`
`B.
`
`C.
`
`Person of Ordinary Skill in the Art (POSA) ........................................................................ 9
`
`Claim Construction.............................................................................................................. 10
`
`Indefiniteness ....................................................................................................................... 11
`
`VI. Yeast Patents............................................................................................................................ 12
`
`A.
`
`B.
`
`Yeast Patents and Prosecution ............................................................................................ 12
`
`POSA for the Yeast Patents ................................................................................................ 12
`
`VII. Technical Background ............................................................................................................ 13
`
`VIII.
`
`Analysis ................................................................................................................................ 16
`
`A.
`
`B.
`
`Term 1: “Promoter Element” .............................................................................................. 16
`
`Term 2: “Mxr1” Terms ....................................................................................................... 20
`
`1.
`A POSA Would Understand Term 2.A to Mean the Sequence Encoding Native Mxr1
`Protein ......................................................................................................................................... 21
`
`2.
`
`“Mxr1” Means Native Mxr1 ........................................................................................... 24
`
`C.
`
`Term 6: “Sequence to Which [the/a] Mxr1 Transcriptional Activator Binds” ................ 31
`
`
`
`
`
`
`
`
`
`
`2
`
`

`

`Case 1:22-cv-00311-WCB Document 345 Filed 02/02/24 Page 3 of 37 PageID #: 22397
`
`I, Dr. Geoffrey Lin-Cereghino, declare as follows:
`
`I.
`
`INTRODUCTION
`
`1.
`
`I have been retained by Quinn Emanuel Urquhart & Sullivan LLP on behalf of
`
`Motif Foodworks, Inc. (“Motif”) as an independent expert in the above-captioned proceeding. I
`
`understand that, in this proceeding (“Litigation”), Impossible accuses Motif of infringing U.S.
`
`Patent Nos. 10,273,492 (Ex. L-1) and 10,689,656 (Ex. L-2) (collectively, the “Yeast Patents”).
`
`2.
`
`As discussed further below, I have been asked to offer my opinion regarding the
`
`meaning of certain claim terms in the Yeast Patents, and to provide my opinion from the
`
`perspective of the person of ordinary skill in the art for the subject matter claimed in the Yeast
`
`Patents (a “POSA”).
`
`3.
`
`I understand that the parties are offering constructions of certain terms in claims 1,
`
`4, 5, 7, and 14 of U.S. Patent No. 10,273,492, and claims 1, 5, 7, 8, 9, 10, 11, 13, 15, 16, 23, 24,
`
`26, and 28 of U.S. Patent No. 10,689,656.
`
`4.
`
`I am being compensated at my customary rate of $250 per hour for my work in this
`
`matter. This compensation is in no way contingent upon the outcome of this matter or upon the
`
`opinions I offer in this declaration. All of the opinions expressed in this declaration are my own.
`
`II.
`
`QUALIFICATIONS AND EXPERTISE
`
`5.
`
`Ex. L-3 accompanying this declaration is a true and correct copy of my current
`
`curriculum vitae. It describes in greater detail my education, publications, employment and
`
`research history, and professional activities and awards.
`
`6.
`
`I am a Professor of Biological Sciences at the University of the Pacific in Stockton,
`
`California. My main responsibilities include: teaching four or more courses per year, supervising
`
`a research laboratory composed of undergraduate and graduate students, and performing various
`
`
`
`3
`
`

`

`Case 1:22-cv-00311-WCB Document 345 Filed 02/02/24 Page 4 of 37 PageID #: 22398
`
`service functions for the University, particularly advising and committee work. Having performed
`
`research on Pichia pastoris since 1997 as a postdoctoral fellow and university professor, I am an
`
`expert in recombinant protein expression in this yeast species. I also have broad training in the
`
`disciplines of microbiology and molecular biology.
`
`7.
`
`I received my Bachelor of Science from the University of California, Davis, in May
`
`1989 where I was selected as a Regents Scholar and graduated with Highest Honors. After working
`
`as an intern and then laboratory biologist in the immunology department at Syntex
`
`Pharmaceuticals, I joined the Ph.D. program at the University of California, San Diego in 1989.
`
`As one of two students in my cohort selected for a predoctoral fellowship from the National
`
`Science Foundation in 1990, I investigated the use of mRNA turnover as a means of gene
`
`regulation in baker’s yeast, Saccharomyces cerevisiae, for my dissertation.
`
`8.
`
`After earning my Ph.D. in 1995, I served as a Visiting Assistant Professor
`
`(sabbatical replacement) at Haverford College for one year, where I continued lab studies in
`
`mRNA turnover with undergraduate research students and taught courses in basic cell biology,
`
`immunology and advanced protein structure.
`
`9.
`
`In 1996, I joined the laboratory of Michael Gold at the Oregon Graduate Institute
`
`of Science and Technology (OGIST) as a postdoctoral research associate, studying the filamentous
`
`fungus Phanerochaete chrysosporium, a fungus used for bioremediation. I was awarded a National
`
`Institute of Environmental Health Sciences Postdoctoral Fellowship and joined the laboratory of
`
`James Cregg, also at OGIST. Dr. Cregg, considered the “father of Pichia,” was one of the first
`
`scientists to develop the molecular tools necessary for using the methylotrophic yeast P. pastoris
`
`as a recombinant protein expression system.
`
`
`
`4
`
`

`

`Case 1:22-cv-00311-WCB Document 345 Filed 02/02/24 Page 5 of 37 PageID #: 22399
`
`10.
`
`Between 1997 and 2000, under Dr. Cregg’s guidance, I pursued an analysis of the
`
`alcohol oxidase I (AOX1) promoter in P. pastoris, culminating with primary authorship on a
`
`publication that identified the transcriptional regulatory protein, methanol expression regulator 1
`
`(Mxr1) protein (“Mxr1p”), which is involved in the control of the AOX1 promoter. See Lin-
`
`Cereghino et al., Mxr1p, a key regulator of the methanol utilization pathway and peroxisomal
`
`genes in Pichia pastoris, 26 Mol. Cell Biol. 883-97 (2006).
`
`11.
`
`During my work in the Cregg lab, I also created plasmids for the expression of
`
`heterologous (non-native) proteins and collaborated with other labs on producing heterologous
`
`proteins in P. pastoris.
`
`12.
`
`In 2000, I became an Assistant Professor at the University of the Pacific (“Pacific”)
`
`in a joint appointment with my wife, Joan Lin-Cereghino. At Pacific, Joan and I have collaborated
`
`for more than two decades on running a research lab dedicated to the expression of recombinant
`
`proteins in P. pastoris.
`
`13.
`
`I have served as a member of the editorial board/associate editor for the journal
`
`Protein Expression and Purification since 2001 and have served as a peer reviewer for several other
`
`journals. I have published 23 articles and reviews on P. pastoris and recombinant protein
`
`expression during my time as a faculty member, including Lin-Cereghino et al., Expression of
`
`foreign genes in the yeast Pichia pastoris, 23 GENETICS ENGINEERING 157-69 (2001); Lin-
`
`Cereghino et al., Condensed protocol for competent cell preparation and transformation of the
`
`methylotrophic yeast Pichia pastoris, 38 BIOTECHNIQUES 44 (2005); Lin-Cereghino & Lin-
`
`Cereghino, Vectors and strains for expression, 389 METHODS IN MOLECULAR BIOLOGY 11-
`
`26 (2007); Hartner et al., Promoter library designed for fine-tuned gene expression in Pichia
`
`pastoris, 36 NUCLEIC ACIDS RESEARCH e76 (2008); Ingram et al., Overcoming Obstacles in
`
`
`
`5
`
`

`

`Case 1:22-cv-00311-WCB Document 345 Filed 02/02/24 Page 6 of 37 PageID #: 22400
`
`Protein Expression in the Yeast Pichia pastoris: Interviews of Leaders in the Pichia Field, 4
`
`PACIFIC JOURNAL OF HEALTH 2 (2021).
`
`14.
`
`I have served as a PI (principal investigator) or co-PI on five federal research grants
`
`from the National Institutes of Health and the National Science Foundation, garnering almost 1.1
`
`million dollars in total, and all involving P. pastoris.
`
`15.
`
`During the past 23 years at Pacific, my wife and I have mentored 25 Masters and
`
`doctoral students as well as 111 undergraduates in our laboratory, all on projects related to P.
`
`pastoris. I have also been dedicated to teaching, which required me to use and expand my expertise
`
`in fungal cell biology and protein expression. In my 23 years at Pacific, for example, I have taught
`
`the course Microbiology, which includes a module about recombinant protein production in P.
`
`pastoris, and I teach about the commercial aspects of P. pastoris expression in my course Industrial
`
`Microbiology.
`
`16.
`
`I am also expected to perform university and professional service as part of my
`
`faculty responsibilities. Along with doing committee work related to open educational resources
`
`and experiential learning, I have evaluated grants for my university as well as some local and
`
`international funding agencies, usually on topics related to recombinant protein expression.
`
`III.
`
`SCOPE OF ASSIGNMENT
`
`17.
`
`I understand that the interpretation of certain terms in the Yeast Patent claims is
`
`disputed in this claim construction proceeding.
`
`18. My understanding of these terms, and the parties’ respective proposed
`
`constructions of these terms, are summarized in the tables below.
`
`
`
`
`
`
`
`
`6
`
`

`

`Case 1:22-cv-00311-WCB Document 345 Filed 02/02/24 Page 7 of 37 PageID #: 22401
`Case 1:22-cv-00311-WCB Document 345 Filed 02/02/24 Page 7 of 37 PagelD #: 22401
`
`Term 1:
`
`Ginkgo/Motif
`
`indefinite
`
`something that modulates, directs or regulates
`
`expression All asserted claims
`
`Term 2:
`
`_“Mxri”Term|Motif,|Ginkgo,|_——Impossible
`
`“a Mxrl “the sequence of the|a sequence of an Mxr1|the consensus
`
`transcriptional
`native P. pastoris
`transcriptional
`sequencethat
`
`
`activator sequence Mxr1transcriptional|activator protein actually binds the
`from P. pastoris”
`activator”
`[Term 2.a]
`[Mxr1] protein
`(492 patent, cl. 1)
`[Term 2.a]
`
`x found naturally in P.
`pastoris [Term 3]
`
`the sequencethatis
`associated with P.
`pastoris [Term 3]
`
`
`
`
`
`“a first exogenous a sequence of an Mxr1|the gene that makes“a first exogenous
`
`
`
`nucleic acid encoding|nucleic acid transcriptional the [Mxrl] protein
`
`
`a methanol expression|sequence ofa native|activator protein [Term 2.b]
`regulator 1 (Mxr1) Mxrltranscriptional|[Term 2.b]
`
`transcriptional
`activator”
`the sequencethatis
`
`activator” x found naturally in P.|associated with P.
`
`(656 patent, cl. 1) pastoris [Term 3] (cl.|pastoris [Term 3]
`7,10, 11, 26, 28
`
`a nucleic acid a sequence of an Mxr1|the gene that makes“a nucleic acid
`
`
`encoding a Mxrl
`encoding the
`transcriptional
`the [Mxrl] protein
`transcriptional
`sequenceof the
`activator protein
`[Term 2.c]
`activator sequence
`native P. pastoris
`[Term 2.c]
`the sequencethatis
`from P. pastoris”
`Mxr1transcriptional
`
`(656 patent, cl. 26) x found naturally in P.|associated with P.activator”
`
`pastoris [Term 3]
`pastoris [Term 3]
`
`Term 6:
`
`indefinite
`
`Ginkgo/Motif
`
`656 patent, all asserted claims
`
`the consensus sequence that actually binds the
`protein
`
`

`

`Case 1:22-cv-00311-WCB Document 345 Filed 02/02/24 Page 8 of 37 PageID #: 22402
`
`
`
`19.
`
`As context for my opinions, I am informed and understand that Impossible and
`
`Motif previously engaged in claim construction briefing regarding the Yeast Patents. I understand
`
`that, in that prior claim construction briefing, Dr. Carl Batt offered declarations on behalf of Motif.
`
`I understand that Dr. Hal Alper offered declarations on behalf of Impossible. I have considered
`
`these declarations.
`
`20.
`
`I am informed and understand that, in July 2023, Impossible sued a second
`
`defendant, Ginkgo Bioworks. I understand that the Court bifurcated the litigation into a parallel
`
`track involving only the Yeast Patents, which are asserted against both Ginkgo and Motif (“Yeast
`
`Case”). I understand that a new claim construction proceeding is ongoing in the Yeast Case and
`
`that this declaration will be submitted in that case. I understand that Ginkgo has submitted an
`
`opening brief in the Yeast Case claim construction proceeding, supported by a declaration of Dr.
`
`Batt (“Batt Declaration” or “Batt Decl.”). I have considered that Batt Declaration as well.
`
`21.
`
`I have been asked to consider the parties’ proposed constructions of Terms 1, 2,
`
`and 6 of the Yeast Patents and provide my independent opinions regarding the meaning of these
`
`terms.
`
`22.
`
`I have also been asked to consider Dr. Batt’s and Dr. Alper’s declarations and to
`
`respond to the Batt Declaration.
`
`23.
`
`I reserve the right to amend or supplement my opinions in this declaration
`
`depending on further developments in the Yeast Case claim construction proceeding, including in
`
`light of any positions Impossible or its expert(s) may offer.
`
`IV.
`
`SUMMARY OF OPINIONS
`
`24.
`
`The bases for my opinions in this declaration are set forth more fully herein. I
`
`summarize them here for convenience.
`
`
`
`8
`
`

`

`Case 1:22-cv-00311-WCB Document 345 Filed 02/02/24 Page 9 of 37 PageID #: 22403
`
`25.
`
`26.
`
`In my opinion, Motif’s proposed constructions of Terms 1, 2, and 6 are correct.
`
`Regarding Term 1, a POSA would not be reasonably certain of the meaning of
`
`“promoter element.” This term has no consistent meaning in the art, and the Yeast Patents do not
`
`describe this term with sufficient clarity such that a POSA would be reasonably certain of whether
`
`any particular structure constituted a “promoter element.” Term 6 is indefinite for similar reasons.
`
`27.
`
`Regarding the individual Term 2 terms, Motif’s proposed constructions align with
`
`how a POSA would understand these terms. To the extent Impossible contends that “Mxr1” does
`
`not mean a sequence encoding a native Mxr1 protein (Mxr1p), that interpretation is inconsistent
`
`with a POSA’s understanding of Mxr1. Additionally, Impossible’s interpretation of Term 2.a as a
`
`Mxr1p binding site, rather than a sequence encoding native Mxr1p, is illogical and unsupported.
`
`28.
`
`In forming my opinion, I have considered the opinions and analysis provided by
`
`Dr. Batt. I agree with Dr. Batt’s opinions and analysis as set forth in this declaration.
`
`V.
`
`LEGAL UNDERSTANDING
`
`29.
`
`In this section I describe my understanding of certain legal principles that I have
`
`relied upon in forming my opinions set forth in this declaration.
`
`30.
`
`I have been informed of these legal standards by counsel for Motif. I am not an
`
`attorney and I have not researched the law on patent invalidity. I am relying only on Motif’s
`
`attorneys relating to these legal standards.
`
`A.
`
`31.
`
`Person of Ordinary Skill in the Art (POSA)
`
`I am informed that patent validity is determined from the perspective of a person of
`
`ordinary skill in the pertinent art at the time of the invention (“POSA”). I understand that a POSITA
`
`is a hypothetical person who is presumed to be aware of all pertinent art, conventional wisdom in
`
`the art, and is a person of ordinary creativity—not an automaton.
`
`
`
`9
`
`

`

`Case 1:22-cv-00311-WCB Document 345 Filed 02/02/24 Page 10 of 37 PageID #: 22404
`
`B.
`
`Claim Construction
`
`32.
`
`I understand that claim construction is a matter of law for the court to decide, but
`
`may be based on underlying facts.
`
`33.
`
`I understand that claim construction begins with the presumption that claim terms
`
`are given their ordinary and customary meaning, and that the ordinary and customary meaning of
`
`a claim term is the meaning that the term would have to a POSA at the time of the invention (i.e.,
`
`the effective filing date)1, viewed in the context of the patent.
`
`34.
`
`I understand that to determine the ordinary and customary meaning of claim terms,
`
`courts may consult a variety of sources, including the claims themselves, the specification, and the
`
`prosecution history (collectively, referred to as “intrinsic evidence”), as well as relevant
`
`dictionaries and treatises, and expert testimony (collectively, referred to as “extrinsic evidence”).
`
`I also understand that intrinsic evidence is the most important source for determining the meaning
`
`of claim terms, but that extrinsic evidence may, in some circumstances, also be useful when
`
`considered in the context of the intrinsic record. I understand that extrinsic evidence cannot be
`
`used to contradict an unambiguous meaning provided in the intrinsic evidence.
`
`35.
`
`I understand that, under some circumstances, a patentee may clearly define a claim
`
`term in the specification or the prosecution history to mean something other than its ordinary
`
`meaning. Similarly, I understand that under some circumstances, a patentee may clearly and
`
`intentionally disclaim certain claim scope within the specification or prosecution history.
`
`36.
`
`I understand that the claim language must be considered in the context of the entire
`
`patent, including the specification and the prosecution history. Specifically, I understand that the
`
`
`1 Like Dr. Batt (Batt Decl. ¶26), I have been asked to assume that the effective filing date
`of the Yeast Patents is May 11, 2015. I reserve the right to offer additional or different opinions
`concerning the effective filing date of the Yeast Patents.
`
`
`
`10
`
`

`

`Case 1:22-cv-00311-WCB Document 345 Filed 02/02/24 Page 11 of 37 PageID #: 22405
`
`usage of a claim term within the specification and prosecution history may provide guidance as to
`
`the patentee’s understanding of the meaning of the term and context which could assist a person
`
`of ordinary skill to ascertain the plain meaning of the claim language. At the same time, I
`
`understand that the specification usually cannot be used to import limitations into the claims, and
`
`that it is also generally improper to read limitations out of the claims.
`
`37.
`
`I further understand that a patent may include two types of claims, independent
`
`claims and dependent claims. An independent claim stands alone and includes only the limitations
`
`it recites. A dependent claim can depend from an independent claim or another dependent claim.
`
`I am informed that a dependent claim includes all the limitations that it recites, in addition to the
`
`limitations recited in the claim from which it depends.
`
`38.
`
`I understand that claim terms should usually be read and understood in a manner
`
`that gives meaning to all of the words in the claim and, further, gives each independent claim a
`
`distinct meaning and scope from its dependent claims. Thus, other claims (and claim elements) of
`
`the patent in question, both asserted and unasserted, can inform the meaning of a claim term. For
`
`example, because claim terms are normally used consistently throughout the patent, the usage of
`
`a term in one claim can often illuminate the meaning of the same term in other claims. Differences
`
`among claims can also be a useful guide in understanding the meaning of particular claim terms.
`
`C.
`
`Indefiniteness
`
`39.
`
`I am informed that patent law requires that the claims of the patent must meet the
`
`definiteness requirement. I understand that a patent is invalid for indefiniteness if its claims, read
`
`in the light of the specification and prosecution history, fail to inform with reasonable certainty a
`
`POSA about the scope of the invention.
`
`
`
`
`
`11
`
`

`

`Case 1:22-cv-00311-WCB Document 345 Filed 02/02/24 Page 12 of 37 PageID #: 22406
`
`VI. YEAST PATENTS
`
`A.
`
`Yeast Patents and Prosecution
`
`40.
`
`I have reviewed the Yeast Patents and their prosecution. I have previously provided
`
`my independent analysis of these patents in a declaration I submitted to the U.S. Patent &
`
`Trademark Office on behalf of Motif in proceedings challenging the validity of the Yeast Patents
`
`(“IPR Declaration”). I attach my IPR Declaration as Exhibit L-4 to this declaration and may refer
`
`to it as necessary. I may offer additional opinions on the Yeast Patents.
`
`41.
`
`I have reviewed Dr. Batt’s description of the Yeast Patents’ specification, claims,
`
`and prosecution. E.g., Batt Decl. §VI.B. From my independent review of the Yeast Patents, I
`
`agree with his characterization as discussed herein.
`
`B.
`
`POSA for the Yeast Patents
`
`42.
`
`Based on my review of the Yeast Patents, the patents are directed to the art of
`
`recombinant protein production. In my opinion, a POSA would have a Bachelor of Science degree
`
`in biochemistry, chemistry, biological sciences, or an equivalent area of study. A POSITA would
`
`also have at least three years of graduate study or professional experience with recombinant
`
`techniques for protein production or general genetic modification experience.
`
`43.
`
`44.
`
`I meet or exceed the qualifications of a POSA for the Yeast Patents.
`
`In rendering my opinions in this declaration, I have applied the perspective of a
`
`POSA for the Yeast Patents as of May 11, 2015.
`
`45.
`
`Dr. Batt’s definition of a POSA for the Yeast Patents is consistent with my
`
`definition (Batt Decl. ¶52).
`
`
`
`
`
`
`
`12
`
`

`

`Case 1:22-cv-00311-WCB Document 345 Filed 02/02/24 Page 13 of 37 PageID #: 22407
`
`VII. TECHNICAL BACKGROUND
`
`46.
`
`I have reviewed Dr. Batt’s description of the technological background of the Yeast
`
`Patents. Batt Decl. §V.
`
`47.
`
`I generally agree with Dr. Batt’s characterization of promoters, though in my
`
`experience inducible promoters may not be totally “off” or “on.” See Batt Decl. ¶40. Rather, their
`
`activity may be strongly decreased or increased in response to external stimuli.
`
`48.
`
`Relatedly, Dr. Batt discusses PpNrg1 as having a negative impact on transcription.
`
`See Batt Decl. ¶49. I agree, though I would refer to PpNrg1 as a “repressor” as it competes with
`
`Mxr1 for binding to certain cites in the promoter of the AOX1 gene.
`
`49.
`
`Dr. Batt cites the “Kranthi” references, which relate to a “consensus” sequence that
`
`Mxr1 protein (Mxr1p) may bind.2 E.g., Batt Decl. ¶44. Per its title, for example, the Kranthi 2009
`
`reference concerns “[i]dentification of key DNA elements involved in promoter recognition by
`
`Mxr1p.” Ex. L-5 (Kranthi 2009), page 460.
`
`50.
`
`The Kranthi 2009 experiments utilize a derivative of Mxr1 rather than the full Mxr1
`
`protein. Specifically, in a section titled “Preparation of recombinant Mxr1p,” Kranthi 2009 teaches
`
`the preparation of a “cDNA encoding the first 150 N-terminal amino acids of Mxr1p,” which
`
`contains a DNA-binding domain. Ex. L-5 (Kranthi 2009), page 461. This cDNA is used to
`
`generate the recombinant Mxr1p protein used in Kranthi 2009’s experiments. As shown in Fig.
`
`1A of Kranthi 2009, however, the first 150 amino acids of Mxr1p represent only a small portion
`
`
`2 Ex. L-5, Kranthi et al., Identification of key DNA elements involved in promoter
`recognition by Mxr1p, a master regulator of methanol utilization pathway in Pichia pastoris, 1789
`Biochimica & Biophysica Acta 4460-468 (2009) (“Kranthi 2009”); Ex. L-6, Kranthi et al.,
`Identification of Mxr1p-binding sites in the promoters of genes encoding dihydroxyacetone
`synthase and peroxin 8 of the methylotrophic yeast Pichia pastoris, 27 Yeast 705-711 (2010)
`(“Kranthi 2010”).
`
`
`
`13
`
`

`

`Case 1:22-cv-00311-WCB Document 345 Filed 02/02/24 Page 14 of 37 PageID #: 22408
`
`of the entire Mxr1 molecule, which is 1155 amino acids long when produced inside a Pichia
`
`pastoris cell. I reproduce this figure below.
`
`
`
`
`
`
`
`
`
`
`
`
`
`51.
`
`Also, Kranthi 2009’s Mxr1p derivative is produced recombinantly in E. coli, a
`
`bacterium, rather than in a yeast. The choice of host cell to produce a recombinant protein matters
`
`because different cell types can process recombinant proteins in different ways. As a review article
`
`(“Gomes”) explains:3
`
`Among the different hosts that are utilized for recombinant protein production, the
`bacteria Escherichia coli is widely known as a preferential host due to the vast
`availability of genetic tools, rapid growth, and simple cultivation techniques.
`Nevertheless, depending on the properties of the desired protein, utilization of E.
`coli might be laborious or not even possible. This is the case when the recombinant
`protein needs to be glycosylated or chemically modified after translation, or
`requires proteolytic processing. Therefore, generally the enzymes purified from E.
`coli need to pass through an in vitro process for the insertion of post-translational
`modifications, which adds steps during protein synthesis, resulting in an even
`costlier process and a reduced yield of final recombinant protein. Thus, as an
`alternative to in vitro modification, eukaryotic hosts such as yeasts, filamentous
`fungi, insects, and plant and mammalian cell lines have been utilized[.]
`
`
`
`52.
`
`After proteins are produced, for example, they may be modified by enzymes present
`
`in the cell. These “post-translational modifications” can affect the structure and activity of
`
`
`3 Ex. L-7, Gomes et al., Comparison of Yeasts as Hosts for Recombinant Protein
`Production, 6 Microorganisms 38 (2018) (“Gomes”), page 2.
`
`
`
`14
`
`

`

`Case 1:22-cv-00311-WCB Document 345 Filed 02/02/24 Page 15 of 37 PageID #: 22409
`
`proteins. For example, Gomes explains (Ex. L-7, page 7, internal footnotes omitted and emphasis
`
`added):
`
`Post-translational modifications involve any process that modifies the protein
`composition. Examples of post-translational modifications (PTMs) consist of the
`reversible addition of a chemical group like phosphate, carbohydrates in
`glycosylation, and polypeptides in ubiquitylation. Additionally, PTM may also
`englobe proteolytic processes during protein maturation or even the modification
`of amino acids such as deamination processes. Those modifications are often
`related to the recombinant protein activity and its direction inside the cell. For
`instance, misleading during PTM modifications may result in miss location [sic] or
`even protein degradation by the ubiquitination pathway. Thus the relevance of
`PTM modification reflects in protein folding and consequently on its biological
`activity.
`
`
`
`53.
`
`As explained above, Kranthi 2009’s Mxr1p derivative is a truncated protein that is
`
`produced in a cell type (E. coli) that cannot modify it in certain ways. This protein is therefore
`
`potentially structurally different in multiple respects from Mxr1 produced in yeast such as P.
`
`pastoris. Accordingly, there are limits on how broadly the teachings of Kranthi 2009 can be
`
`extrapolated to show the activity of Mxr1p itself, particularly the activity of Mxr1p that is produced
`
`in yeast cells.
`
`54.
`
`I believe it is helpful to note the limitation of the Kranthi 2009 experiments because,
`
`for example, these limitations may explain certain results which may otherwise appear
`
`inconsistent.
`
`55.
`
`For example, as Dr. Batt explains, Mxr1p does not always bind to the “consensus”
`
`sequence. This is shown in Kranthi (2010), as I discuss further below with respect to Term 1
`
`(“promoter element”).
`
`56.
`
`In Dr. Batt’s words, “while these [consensus] sequences may be necessary for
`
`Mxr1p binding, they are not sufficient for it.” See Batt Decl. ¶128. I agree. It has been shown
`
`that the Mxr1 DNA-binding domain (i.e., Kranthi’s truncated Mxr1p protein produced in E. coli)
`
`
`
`15
`
`

`

`Case 1:22-cv-00311-WCB Document 345 Filed 02/02/24 Page 16 of 37 PageID #: 22410
`
`recognizes and binds the consensus sequence in the context of certain promoters (or pieces
`
`thereof). But the presence of the consensus sequence in any string of nucleic acids is not sufficient
`
`to cause Mxr1p binding.
`
`57.
`
`The factors that may cause Mxr1p to bind to the consensus sequence in some cases,
`
`but not others, remain poorly understood. These factors must be determined empirically and
`
`cannot be predicted beforehand.
`
`58.
`
`Thus, I agree with Dr. Batt’s characterization of the relevant technical background
`
`of the Yeast Patents as discussed herein. His characterization is consistent with my prior opinions
`
`and analysis concerning the technical background of the Yeast Patents set forth in my IPR
`
`Declaration, which I incorporate herein. I reserve the right to offer additional opinions on
`
`technology concerning the Yeast Patents at a later date, if necessary.
`
`VIII. ANALYSIS
`
`A.
`
`Term 1: “Promoter Element”
`
`59. My understanding of the parties’ proposed constructions for the term “promoter
`
`element” (“Term 1”) is set forth above. I understand that Motif and Ginkgo contend that this term,
`
`which is recited in all claims of the Yeast Patents, is indefinite. In contrast, I understand Impossible
`
`contends that this term means something that modulates, directs or regulates expression.
`
`60.
`
`61.
`
`As explained below, in my opinion, Motif and Ginkgo’s interpretations are correct.
`
`Additionally, I have reviewed Dr. Batt’s analysis of the term “promoter element”
`
`in the Batt Declaration and in his declarations previously submitted in this Litigation’s claim
`
`construction proceedings. E.g., Batt Decl. ¶¶62-78. As explained below, I agree with Dr. Batt
`
`that a POSA would not be reasonably certain of the scope of a “promoter element,” as that term is
`
`used in the context of the Yeast Patent claims.
`
`
`
`16
`
`

`

`Case 1:22-cv-00311-WCB Document 345 Filed 02/02/24 Page 17 of 37 PageID #: 22411
`
`62.
`
`Promoters are well-understood to contain binding sites for transcriptional activators
`
`to bind and initiate gene expression. As a matter of linguistic clarity and common sense, a POSA
`
`would understand that the addition of the term “element” changes the scope of a promoter to refer
`
`to some smaller portion of the promoter. From my review of the Yeast Patent specifications, they
`
`likewise distinguish “promoters” from “promoter elements” within those promoters. I reproduce
`
`below a few representative quotations from the patents where this distinction is made.
`
`There are a number of inducible promoters that can be used when genetically
`engineering methylotrophic yeast. For example, a methanol-inducible promoter, or
`a promoter element therefrom, can be used. Methanol inducible promoters are
`known in the art. For example, a commonly used methanol-inducible promoter
`from P. pastoris is the promoter, or a portion thereof, from the alcohol oxidase 1
`(AOX1) gene, which is strongly transcribed in response to methanol. Other
`methanol-inducible promoters, or promoter elements therefrom, however, can be
`used, including, without limitation, the alcohol oxidase (AOD1) promoter from
`Candida boidinii (see, for example, GenBank Accession No. YSAAOD1A), the
`alcohol oxidase (MOX) promoter from Hansenula polymorpha (see, for example,
`GenBank Accession No. X02425), the MOD1 or MOD2 promoter from Pichia
`methanolica (see, for example, Raymond et al., 1998,