Case 1:22-cv-00311-WCB Document 354 Filed 02/09/24 Page 1 of 20 PageID #: 22905
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`IN THE UNITED STATES DISTRICT COURT
`FOR THE DISTRICT OF DELAWARE
`
`
`Plaintiff,
`
`
`
`v.
`
`
`
`Defendants.
`
`
`
`
`C.A. No. 22-311-WCB
`
`JURY TRIAL DEMANDED
`
`
`
`))))))))))
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`
`
`IMPOSSIBLE FOODS INC.,
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`
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`
`
`MOTIF FOODWORKS, INC. and
`GINKGO BIOWORKS, INC.,
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`
`
`DECLARATION OF HAL ALPER, PH.D. IN SUPPORT OF IMPOSSIBLE FOODS
`INC.’S SUR-REPLY CLAIM CONSTRUCTION BRIEF
`
`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
`(206) 883-2529
`
`
`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: February 9, 2024
`11318533 / 20200.00002
`
`
`
`
`
`
`
`

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`Case 1:22-cv-00311-WCB Document 354 Filed 02/09/24 Page 2 of 20 PageID #: 22906
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`
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`I.
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`II.
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`TABLE OF CONTENTS
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`Page
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`PRIOR DECLARATIONS ................................................................................................. 1
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`SUPPLEMENTATION OF OPINIONS ............................................................................ 1
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`A.
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`B.
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`C.
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`D.
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`Term 1—“Promoter Element” ................................................................................ 1
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`Term 2—“a Mxr1 transcriptional activator sequence” / “a methanol
`expression regulator 1 (Mxr1) transcriptional activator” / “a Mxr1
`transcriptional activator sequence” ....................................................................... 12
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`Term 3—“from P. pastoris” ................................................................................. 15
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`Term 6—“sequence to which [the/a] Mxr1 transcriptional activator binds” ........ 17
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`III.
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`CONCLUSION ................................................................................................................. 18
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`
`
`i
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`

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`Case 1:22-cv-00311-WCB Document 354 Filed 02/09/24 Page 3 of 20 PageID #: 22907
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`I, Hal Alper, Ph.D., submit this declaration in support of plaintiff Impossible Foods Inc.’s
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`(“Impossible”) Claim Construction Sur-Reply Brief. I offer this declaration as an expert in the
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`fields of genetic engineering, synthetic promoter design, yeast engineering, and synthetic
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`biotechnology. My qualifications and experience in these areas among others are set out in my
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`June 14, 2023 Declaration (D.I. 107) and my curriculum vitae (D.I. 107-1, Ex. A).
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`I.
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`PRIOR DECLARATIONS
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`1.
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`I incorporate here my three prior declarations regarding these claim terms in U.S.
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`Patent Nos. 10,689,656 (the “’656 patent”) and 10,273,492 (the “’492 patent”) (the “Yeast
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`Patents”). The first is dated June 14, 2023, the second is dated July 7, 2023, and the third is
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`dated January 26, 2024. D.I. 107, 144, 339.
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`2.
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`I discussed the claim terms that I discuss here in my prior declarations and
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`provided analysis and evidence regarding how a person of ordinary skill in the art (“POSA”)
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`would understand them. I supplement those analyses here with an effort not to repeat what I
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`have already discussed.
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`3.
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`As I have noted previously, Dr. Batt and Dr. Lin-Cereghino made statements in
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`their IPR declarations that are consistent with my opinions. I have cited select references below.
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`4.
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`I also note that much of Dr. Batt’s and Dr. Lin-Cereghino’s testimony is
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`duplicative of what was said in earlier declarations. I previously explained the basis for my
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`disagreement. D.I. 107, 144, 339.
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`II.
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`SUPPLEMENTATION OF OPINIONS
`A.
`
`Term 1—“Promoter Element”
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`5.
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`My testimony regarding the meaning of “promoter element” remains consistent.
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`As discussed in my previous declarations, a POSA would understand “promoter element” to
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`refer to “a polynucleotide that regulates (e.g., drives) transcription of a polynucleotide sequence
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`Case 1:22-cv-00311-WCB Document 354 Filed 02/09/24 Page 4 of 20 PageID #: 22908
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`(e.g., gene),” and that “a promoter element is upstream of, and adjacent to or in close physical
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`proximity to the gene.” D.I. 338 at 1. My opinion derives from the claim language,
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`specification, and file history of the Yeast Patents. This definition is also consistent with the
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`understanding of a POSA as well as the literature in the field, including papers I have authored.
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`6.
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`Dr. Batt incorrectly claims that my positions have changed. They have not. Dr.
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`Batt’s opinion in this regard is based on a false distinction between what a “promoter element” is
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`and what it does. I also note that Dr. Batt’s opinion appears to be based on the notion that
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`because not all possible promoter elements are fully characterized in the literature, a POSA
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`would not know what a promoter element is. I disagree. As I explained previously, a POSA
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`would have knowledge of genetic engineering and would be well-aware of promoters, the
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`structural relationship of promoter elements within promoters and their utility in driving
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`transcription of recombinant nucleic acids. D.I. 107, 144, 339.
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`7.
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`As I explained in my earlier declarations, a POSA would have known from the
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`literature several examples of promoter elements that function to drive transcription of nucleic
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`acids encoding proteins. E.g., D.I. 123-1 at Ex. B22 (Hartner 2008); D.I. 339-1 at Ex. 2
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`(Redden); D.I. 341-1, Ex. L-5 (Kranthi 2009); D.I. 341-1, Ex. L-6 (Kranthi 2010); D.I. 341-1,
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`Ex. L-10 (Motif IPR Lin-Cereghino Exhibit); Ex. 1 (Old, R.W. & S.B. Primrose, “Cloning in
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`Saccharomyces cerevisiae and other microbial eukaryotes,” Principles of Gene Manipulation: An
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`Introduction to Genetic Engineering, 257-258 (N.G. Carr ed., 5th ed. 1994)). If the function of a
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`specific promoter element is not fully characterized in the literature, a POSA would know how to
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`verify that it drives transcription of downstream proteins. E.g., D.I. 123-1 at Ex. B22 (Hartner
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`2008); D.I. 339-1 at Ex. 2 (Redden); D.I. 341-1, Ex. L-5 (Kranthi 2009); D.I. 341-1, Ex. L-6
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`(Kranthi 2010); D.I. 341-1, Ex. L-10 (Motif IPR Lin-Cereghino Exhibit); Ex. 1 (Old, R.W. &
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`2
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`S.B. Primrose). A POSA would certainly know how to construct, test, evaluate, and deploy both
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`native and synthetic promoters derived from organisms such as P. pastoris. E.g., D.I. 123-1 at
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`Ex. B22 (Hartner 2008) at 2. Furthermore, a POSA would certainly understand (as demonstrated
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`by a 2008 paper in which Dr. Lin-Cereghino is a co-author) that even without a complete
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`molecular biology understanding of the exact molecular mechanism of transcription factor
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`binding, synthetic promoters derived from the P. pastoris AOX1 promoter element could be
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`established and the “approach of predicting putative TFBSs [transcription factor binding sites]
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`followed by deletion or duplication of the respective region within the promoter sequence was
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`highly successful in generating a library spanning a broad range of activities.” D.I. 123-1 at Ex.
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`B22 (Hartner 2008) at 12. For at least these reasons, not only would a POSA understand the
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`meaning of “promoter element” with reasonable certainty, but a POSA would also be able to
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`ascertain how to manipulate these promoters, move transcription factor binding sites, and utilize
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`these promoters to express genes of interest.
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`8.
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`There appears to be no disagreement that promoter elements were known in the
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`art. For example, promoter elements are evident from Dr. Batt’s discussion of the transcription
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`process. D.I. 334 (Batt January), ¶ 41.
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`9.
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`Dr. Batt depicts the interaction of two promoter elements: an upstream activator
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`sequence and a core promoter element. The upstream activator sequence (UAS) has recognition
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`sequences for transcriptional activators (e.g., Mxr1) and the core promoter element is bound by
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`3
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`the RNA polymerase complex. Together the UAS and the core promoter element drive
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`transcription. While the illustrated UAS is simplified to reflect only a single activator binding
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`site, Dr. Batt acknowledges that UAS would have multiple binding sites for transcriptional
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`activators. D.I. 334 (Batt III), ¶ 42.
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`10.
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`Dr. Batt describes the TATA box in his first declaration and suggests that it might
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`be a promoter element. D.I. 123 (Batt I), ¶¶ 156-160. However, Dr. Batt also acknowledges that
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`the TATA box is merely the sequence that suggests where transcription begins. Id., ¶ 157. That
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`is, the TATA box is the starting point for a process regulated by sequences upstream of it such as
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`UAS and core promoter elements.
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`11.
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`Dr. Batt acknowledges that it is possible to identify “elements” of a promoter with
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`a role in the promoter’s activity. D.I. 123 (Batt I) at 45, n.2. I agree. However, I disagree with
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`Dr. Lin-Cereghino’s and Dr. Batt’s assertion that “promoter element” is used inconsistently in
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`the scientific literature. While there may be some context-dependent variation in use of the term
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`promoter element, such various contexts do not alter the objective understanding of the phrase in
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`the field, especially when it is used in the context of expressing or producing a protein from a
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`gene.
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`12.
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`Indeed, as Dr. Batt concedes, yeast promoters, such as AOX1, have been heavily
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`studied and well-characterized, and their functional elements are readily known to a POSA.
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`D.I. 142-1 at Ex. 23 (Batt IPR Declaration), ¶ 81 (“The AOX1 promoter is regarded as the ‘the
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`most commonly used promoter for heterologous protein expression in P. pastoris.’ The AOX1
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`promoter has been ‘well-characterized’, is available in commercial kits, and is ‘employed in
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`most studies and applications’ of the P. pastoris expression system.”). Such functional elements
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`of the AOX1 promoter are specifically recited in the Yeast Patent claims.
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`4
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`13. Moreover, Dr. Batt fails to consider that the language of the claims creates a
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`relationship between “promoter element” and the nucleic acid encoding a protein to which it is
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`operably linked. Thus, the context of the claims would inform a POSA that “promoter element”
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`refers to a functional portion of a promoter which (along with the Mxr1 transcriptional activator
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`sequence) drives transcription of the nucleic acid to which it is operably linked. “Promoter
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`element linked to a gene” for the purpose of gene transcription is an unambiguous, commonly
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`understood terminology that a POSA would immediately recognize—this use of the term
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`underscores the function of this element, i.e., to drive expression of the desired gene.
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`Accordingly, hypotheticals such as “would 2 base pairs be a promoter element” are meaningless
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`if you actually want to express the gene.
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`14.
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`Dr. Batt argues the relationship between promoter structure (e.g., sequence and
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`location thereof) and promoter function (e.g., effect on gene expression) is determined
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`empirically. D.I. 123 (Batt I), ¶ 165. Even if that notion were accepted, it does not change that a
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`POSA would know (1) the identity of many promoter elements and their functionality; and
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`(2) how to determine if a previously uncharacterized promoter element were functional in the
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`recombinant nucleic acid expression construct of the claims. D.I. 123-1 at Ex. B20 (Vogl 2013);
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`D.I. 123-1 at Ex. B22 (Hartner 2008). A POSA would certainly understand that some amount of
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`experimentation may be necessary when developing previously uncharacterized gene expression
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`systems. This was (and continues to be) routine in the field of molecular biology and
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`biotechnology. Nevertheless, a POSA would certainly understand how to create such expression
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`systems in the context of the Yeast Patents and their teachings.
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`15.
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`Contrary to the assertions in Dr. Batt’s declaration, I use the word “structural” in
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`the same sense he does. The term “structural” describes the physical properties of promoter
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`5
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`elements such as their sequence and their physical arrangement both within a recombinant
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`nucleic acid expression construct and in relation to the nucleic acid whose transcription they
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`control.
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`16.
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`Dr. Batt asserts that I have not opined on the scope of “promoter element.” This
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`is incorrect. As I explained previously, a “promoter element” is a functional portion of a
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`promoter which can be used to enable transcription. Dr. Batt and I agree that the Yeast Patents
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`are directed to a protein expression system and that promoter elements are necessary for
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`transcription. The Yeast Patents further discuss the use of inducible and constitutive promoters
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`and promoter elements therefrom in expressing proteins. Further, a POSA would have been
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`well-aware of “promoter elements” and their utility in expression of recombinant proteins in
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`transgenic yeast. D.I. 142-1 at Ex. 23 (Batt IPR Declaration), ¶ 63 (“[S]cientists have described
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`P. pastoris as having ‘become the premier example of yeast species used for the production of
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`recombinant proteins.’”). Dr. Batt’s insistence that a POSA would not understand this term with
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`reasonable certainty ignores both the Yeast Patents and a POSA’s knowledge in the field.
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`17.
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`Dr. Batt asserts “[c]ontext—including the surrounding sequences, the locations of
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`those sequences relative to a gene to be expressed, and the host organism—plays a significant
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`role in whether any particular sequence will perform the function of ‘promoter element[.]’” D.I.
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`347 (Batt IV), ¶ 10. This does not negate that a POSA would know, with reasonable certainty,
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`what a promoter element is and how to measure its function. As I pointed out in my previous
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`declarations, there were many well-characterized promoter elements known in the art and a
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`POSA would have known how to manipulate promoter elements to drive transcription of
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`recombinant nucleic acids. Furthermore, Dr. Batt has previously indicated he understands
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`“promoter element” without defining context. D.I. 142-1 at Ex. 23 (Batt IPR Declaration), ¶ 136
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`6
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`(“The expected consequence of this design is that, as Mxr1 levels increase in the nucleus of the
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`host methylotrophic yeast cell, Mxr1 increases its own expression by binding to the methanol-
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`inducible promoter element in the recombinant nucleic acid molecule.”) (emphasis added).
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`18.
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`Furthermore, as described above, even Dr. Lin-Cereghino’s highlights the
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`advanced understanding in the art of how to deploy the knowledge of promoter elements to the
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`development of synthetic promoters using Mxr1 binding sites. The art-known methods of
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`building synthetic promoter elements implies a firm understanding of, at minimum, identifying
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`and using promoter elements.
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`19.
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`I disagree with Dr. Batt’s opinion that the specification of the Yeast Patents does
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`not provide guidance regarding the scope of the claim term “promoter element.” As I have
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`discussed before, the specification of the Yeast Patents teaches that promoters and promoter
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`elements are expression elements. The ’656 patent indicates that “‘operably linked’ means that a
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`promoter or other expression element(s) are positioned relative to a nucleic acid coding sequence
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`in such a way as to direct or regulate expression of the nucleic acid[.]” ’656 patent at 4:47-51
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`(emphasis added). This definition is completely in line with the plain and ordinary meaning of
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`the term “promoter element,” as I have discussed above and in my prior reports. The ’656 patent
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`further provides that “[e]xpression elements include nucleic acid sequences that direct and
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`regulate expression of nucleic acid coding sequences. One example of an expression element is
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`a promoter sequence. Expression elements also can include introns, enhancer sequences,
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`response elements, or inducible elements that modulate expression of a nucleic acid[.]” ’656
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`patent at 9:66-10:8.
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`20.
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`In my opinion, a POSA would understand that “expression elements” include
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`promoters and promoter elements as expressly described in the specification. For example,
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`7
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`“inducible elements” include upstream activator sequences that respond to the presence of
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`methanol. Ex. 1 (Old and Primrose), 257-258. An exemplary methanol-inducible element is
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`present in the AOX1 promoter which binds Mxr1 (among other proteins) to facilitate
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`transcription. D.I. 341-1, Ex. L-6 (Kranthi 2010). These inducible elements can even be
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`transferred to other non-inducible basal elements to impart inducibility. This transferability
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`showcases function.
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`21.
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`Furthermore, my opinion regarding the construction of “promoter element” does
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`not render the term “operably linked” meaningless. In the context of the claims, “operably
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`linked” refers to the relationship between the promoter element and the recited nucleic acid
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`encoding a protein. The claims describe both a physical location and functional interaction
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`between the promoter and the nucleic acid. Operably linked requires that the recited promoter is
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`driving expression of the recited nucleic acid.
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`22.
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`Dr. Batt takes issue with my opinion that a “promoter element” may drive
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`transcription and not that it must do so. My opinion is in accord with the basic biology of
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`transcription as well as the context of the claims. For example, a promoter element may need to
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`be combined with a transcription factor (recited in the claims) or operatively linked to the nucleic
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`acid being transcribed (recited in the claims) or provided with an inducing media like methanol
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`(recited in the claims) before transcription occurs. Neither biology nor the claims require that a
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`promoter element in isolation drive transcription. Indeed, if a promoter element were not
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`operably linked to a coding sequence, it would not function to create a downstream protein.
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`23.
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`Dr. Batt takes issue with the Yeast Patents’ disclosure that “constitutive promoters
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`and constitutive promoter elements are known in the art.” While agreeing that constitutive
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`promoters were known, he disagrees that constitutive promoter elements were known in the art
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`8
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`on the basis that “there is no consensus understanding as to what a ‘constitutive promoter
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`element’ is in vacuo.” D.I. 347 (Batt IV), ¶ 13. But the Yeast Patents do not use the term
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`“promoter element” in vacuo, it is used in the context of the invention—that is, expression of
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`recombinant nucleic acids in methylotrophic yeast cells. It is in this context and within the
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`claims of the Yeast Patents that a POSA would understand the scope of the term. Whether the
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`term has a definition in vacuo is beside the point, and a POSA would certainly understand this.
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`24.
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`Dr. Batt’s opinions are predicated on the notion that the specification and claims
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`need to identify a specific sequence for a POSA to understand the meaning of “promoter
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`element.” This is false. Considering the state of the art, a POSA would have understood the
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`meaning of “promoter element,” including the role of promoter elements in driving expression of
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`recombinant proteins that the Yeast Patents describe. This understanding was the underpinning
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`of basic molecular biology and modern biotechnology before the priority date and was
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`instrumental in ushering in the recombinant DNA technology era.
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`25.
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`As an example of the state of the art, the Hartner paper—which is co-authored by
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`Dr. Lin-Cereghino—describes genetic engineering of the AOX1 promoter from P. pastoris. D.I.
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`123 at B22 (Hartner 2008). The paper describes genetically engineering promoters to “fine-
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`tune” expression of recombinant proteins in Pichia pastoris. Id. at Abstract (“[T]he new PAOX1
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`synthetic promoter library constitutes a basic toolbox to fine-tune gene expression in metabolic
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`engineering and sequential induction of protein expression in synthetic biology.”). For example,
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`the paper discusses that functional elements may be added, taken away, or swapped out to create
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`new promoters with different properties. Id. at 7 (discussing deletions), 8 (discussing additions),
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`10 (discussing use of core promoter elements from promoters other than AOX1). As reflected in
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`the Hartner paper, promoter elements are modular. Id. at 2 (“provide elements for a modular
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`9
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`synthetic promoter design”), 10 (“using modular building blocks, several cis-acting elements . . .
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`were added to different basal promoters”) (emphasis added). Accordingly, Hartner amply
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`supports my opinion that not only did POSAs know what promoter elements are, but they also
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`knew how to engineer them to improve expression of recombinant proteins in Pichia pastoris.
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`Moreover, as I have explained previously, the knowledge in the field improved significantly after
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`the Hartner paper, as reflected in other literature. D.I. 339.
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`26.
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`Another even earlier paper by Hartner (published in 2006), which Dr. Batt
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`discussed in his IPR declarations, similarly supports my opinion that “promoter element” was
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`consistently and routinely used in the literature regarding recombinant protein expression in
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`yeast. Ex. 2 (Hartner 2006). Hartner notes, “The major application of methylotrophic yeasts is
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`recombinant protein production. As reviewed extensively, promoter elements derived from
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`genes involved in methanol utilization, especially the alcohol oxidase promoters, have been
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`utilized to express several hundreds of different proteins in methylotrophic yeasts so far.” Id. at
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`2. Hartner presents a graphic of functional elements in various promoters that had been
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`characterized at that time (id. at 11):
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`10
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`27.
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`Dr. Batt focuses on the functional nature and breadth of “promoter element” and
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`alleges these properties render the term indefinite. I disagree. Neither the functional nature of
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`promoter elements nor the breadth of the term alters the conclusion that a POSA would
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`understand the scope with reasonable certainty. Dr. Batt acknowledges that “promoter element”
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`is a term understood by a POSA and acknowledges descriptions of exemplary promoter elements
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`in the literature. The use of “promoter element” in the literature is consistent with its use in the
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`Yeast Patent specification. Thus, there is no disagreement that a POSA would have knowledge
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`of promoter elements, including assays for experimentally verifying their function. Far from
`
`being a term of uncertain scope, POSAs understood both what promoter elements are and how to
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`identify them along with their functions. D.I. 339-1 at Ex. 2 (Redden); D.I. 123-1 at Ex. B22
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`(Hartner 2008).
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`28.
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`POSAs were well-versed in the identification and manipulation of promoter
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`elements, a routine aspect of recombinant protein expression. Dr. Batt confirms as much in his
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`IPR declaration. Dr. Batt pointed to the Tsutsumi reference and explained that it discloses the
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`use of recombinant methods to express a protein in “yeast cells under the control of a promoter
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`element.” D.I. 142-1 at Ex. 23 (Batt IPR Declaration), ¶ 141. Tsutsumi discloses, for example,
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`an “improved DAS promoter” which comprises “a functional part” of the DAS promoter from P.
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`pastoris and upstream sequences with binding sites for transcriptional activators (e.g., Mxr1,
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`Prm1). Ex. 3, (Tsutsumi), claim 1, Figure 3, ¶¶ 8 (“the DAS promoter sequence from Pichia or a
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`functional part thereof”), 37, 40-69, 137. I agree with Dr. Batt that this functional part of the
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`DAS promoter is a “promoter element.”
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`11
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`B.
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`Term 2—“a Mxr1 transcriptional activator sequence” / “a methanol
`expression regulator 1 (Mxr1) transcriptional activator” / “a Mxr1
`transcriptional activator sequence”
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`29.
`
`I note that Dr. Lin-Cereghino collapses Term 2 and Term 3 and argues Term 2a
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`“means the sequence of the native P. pastoris Mxr1 transcriptional activator (Mxr1p).” I will
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`address Dr. Lin-Cereghino’s arguments regarding “native” with Term 3.
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`30.
`
`As discussed in my prior declarations and above, Mxr1 consensus binding sites
`
`were known in the art. Dr. Batt misinterprets the Yeast Patents, specifically how the claim term
`
`“operably linked” relates to a promoter element and an Mxr1 transcriptional activator sequence
`
`from P. pastoris.
`
`31.
`
`Dr. Batt asserts that the claims require a nucleic acid molecule encoding, for
`
`example, a “heme-containing protein/polypeptide involved in heme biosynthesis” and an Mxr1
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`protein. This interpretation is not supported by the plain language of the claims nor the
`
`specification. Dr. Batt does not point to any description in the specification where a nucleic acid
`
`encodes Mxr1 but lacks an operative linkage to a promoter element.
`
`32.
`
`The specification does, however, describe nucleic acid molecules in accord with
`
`my understanding of the claims. For example, the specification describes a nucleic acid
`
`molecule encoding a heme-containing protein (e.g., LegH) operably linked to the AOX1
`
`promoter. E.g., ’656 patent at Figure 2, (“A plasmid containing two copies of the soybean LegH
`
`gene (sequence optimized for P. pastoris; SEQ ID NO:3) under the control of the pAOX1
`
`promoter . . . ”). It also describes various nucleic acid molecules encoding a polypeptide
`
`involved in heme biosynthesis (e.g., UPD, CPO, UPS, ALA synthase, PPG oxidase,
`
`porphobilinogen deaminase) operably linked to the AOX1 promoter. E.g., ’656 patent at Figure
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`2, (“Each gene was placed under control of the AOX1 promoter . . . [.]”). The literature—
`
`including literature cited by Dr. Batt—reflects that the AOX1 promoter comprises promoter
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`
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`elements and an Mxr1 transcriptional activator sequence (i.e., the sequence to which the Mxr1
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`transcriptional activator protein binds). E.g., D.I. 123-1 at Ex. B22 (Hartner 2008).
`
`33. Moreover, as I discussed above, the phrase “operably linked” applies to the
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`relationship between a protein to be expressed and promoters and expression elements driving
`
`the gene responsible for said protein expression. The specification states that expression
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`elements are “nucleic acid sequences” and include “enhancer sequences, response elements, or
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`inducible elements that modulate expression of a nucleic acid.” ’656 patent at 2:4-11 and 9:66-
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`10:8. Inducible elements include upstream activator sequences that respond to the presence of
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`methanol. Id. at 4:52-5:11. A POSA would have understood that the upstream activator
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`sequence of AOX1 is an inducible element which binds Mxr1 (among other proteins) to facilitate
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`transcription. D.I. 123-1 at Ex. B22 (Hartner 2008); D.I. 123-1 at Ex. B20 (Vogl 2013).
`
`34.
`
`Thus, my interpretation of the claims—that a nucleic acid encoding a protein
`
`(heme or heme biosynthesis protein) is operably linked to (1) a promoter element and (2) an
`
`Mxr1 binding site—is wholly supported by the specification. In contrast, Dr. Batt’s
`
`interpretation—that a nucleic acid encoding a protein (heme or heme biosynthesis protein) is
`
`operably linked to a promoter element, and there also is an Mxr1 protein encoded, but not
`
`necessarily operatively linked to a promoter element—is not how a POSA would interpret the
`
`claims. Moreover, as I have stated before, Dr. Batt’s interpretation results in two different
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`phrases in claim 14 (colored green and red, below) meaning the same thing:
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`Case 1:22-cv-00311-WCB Document 354 Filed 02/09/24 Page 16 of 20 PageID #: 22920
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`’492 Patent
`Claims 1 and 14
`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.
`
`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.
`
`Plain and Ordinary
`Meaning
`
`Defendants’
`Construction
`
`
`
`
`
`
`Mxr1 protein binds
`here
`
`
`
`
`Mxr1 protein binds
`here
`
`Sequence encoding
`Mxr1
`
`
`Mxr1 protein binds
`here
`
`
`
`
`
`
`Sequence
`encoding Mxr1
`
`
`
`
`Sequence
`encoding Mxr1
`
`Sequence
`encoding Mxr1
`
`
`Sequence
`encoding Mxr1
`
`35.
`
`Dr. Batt argues that assigning the same meaning to different words is appropriate.
`
`I disagree. Dr. Batt’s reliance on discussion in the Yeast Patents of using a single promoter to
`
`drive expression of two proteins does not justify giving the same meaning to different claim
`
`terms. The specification does not explain why the same concept would be expressed in different
`
`language. This is especially true in view of my opinions above regarding the interpretation of
`
`claim 1. Accordingly, my opinion is that a POSA would interpret the different phrases in claim
`
`14 to have different meanings.
`
`36.
`
`Dr. Lin-Cereghino offers opinions based on his interpretation of “simple English.”
`
`D.I. 338-1 (Lin-Cereghino Declaration, ¶ 80). I disagree. Moreover, as I explain above and in
`
`14
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`Case 1:22-cv-00311-WCB Document 354 Filed 02/09/24 Page 17 of 20 PageID #: 22921
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`my prior declarations, based on my expertise in the technology discussed in the Yeast Patents,
`
`Dr. Lin-Cereghino’s linguistic argument fails to account for the technical aspects of the claims.
`
`37.
`
`Dr. Lin-Cereghino also opines that the claims reciting “a nucleic acid molecule
`
`encoding a heme-containing protein operatively linked to . . . a Mxr1 transcriptional activator
`
`sequence” and another promoter element “would be confusing to a POSA.” I disagree. As I
`
`explained above, a “promoter element” is broader than just an Mxr1 binding site, and the Yeast
`
`Patents describe operable linkage of nucleic acids encoding proteins to promoter elements and
`
`other expression elements, which include Mxr1 binding sites. This is not confusing to a POSA.
`
`38.
`
`Dr. Lin-Cereghino also opines that the Yeast Patents do not describe transcription
`
`factor binding. For the reasons I discuss below with respect to Term 6, I disagree.
`
`C.
`
`39.
`
`Term 3—“from P. pastoris”
`
`As discussed in my prior declarations, “from P. Pastoris” and “from Pichia
`
`pastoris” indicates to a POSA that a given sequence has its origins in the Pichia pastoris
`
`genome. However, this claim term does not indicate that the sequence must be identical at every
`
`single base pair to that of the Pichia pastoris genome—it encompasses genetic engineering and
`
`natural variation.
`
`40.
`
`Dr. Lin-Cereghino modifies the claim to require the given sequence to be “native”
`
`to P. pastoris. The claims are not so limited as I explained in earlier declarations. The Yeast
`
`Patents consistently characterize sequences “from” a particular genus and