DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Elections/Restrictions
Applicant's election of Group I, claims 1-9 drawn to a cell or plant comprising the cell, wherein the cell is engineered to express or overexpress an enzyme in the reply filed on 06/05/2026 is acknowledged. Because Applicants did not distinctly and specifically point out supposed errors in the restriction requirement, the election has been treated as an election without traverse. See MPEP § 818.03(a).
Claims 10-20 are withdrawn from further consideration for being directed to a nonelected inventions.
Priority
Acknowledgment is made of applicant’s claim for priority to U.S. Provisional Application No. 63/588,272, filed October 5th, 2023.
The effective filing date is October 5th, 2023.
Information Disclosure Statement
The information disclosure statements (IDS) submitted on 10/09/2024 are acknowledged and are being considered by the examiner.
Status of the Claims
Claims 1-20 are pending.
Claims 10-20 are withdrawn.
Claims 1-9 are examined herein.
Claim Objections
Claims 1-2 are objected to because of the following informalities:
The claims lack a comma preceding the conjunction in a list of more than 2 items (e.g., claim 1 line 3 recites “(SvDHS1b) or a DHS1b enzyme” instead of “(SvDHS1b), or a DHS1b enzyme”).
Appropriate correction of the above informalities is required.
Claim Interpretations
Regarding claims 1-9, the term “engineered” is defined in the Specification para 0038 as “meaning that they have been altered by the hand of man.”
Regarding claims 1-9, Specification para 0192 recites “four different grass species [ and their abbreviations within parenthesis]: Brachypodium distachyon (Bd), Oryza sativa (Os), Sorghum bicolor (Sb), and Setaria viridis (Sv).” Thus, the first two alphabetic letters in each instance of alphanumeric text within parenthesis as recited in claims 1 and 2 are interpreted as indicating which species the protein/enzyme (i.e., the rest of the text within the parentheses recited in claims 1-2) belongs to.
Regarding claims 1-9, the term “DHS1b’ refers to “the first enzyme in AAA [aromatic amino acid] biosynthesis, 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase (DHS; EC:2.5.1.54)” and the term “Tyra” as recited in claims 1-2 refers to an enzyme “controlling tyrosine and phenylalanine biosynthesis from arogenate, arogenate dehydrogenase (TyrA; EC 1.3.1.78)” (specification, para 0068).
Claim Rejections - 35 USC § 112(b)
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1-9 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention. All dependent claims are included in these rejections unless they contain a limitation that overcomes the deficiencies of the parent claim from which they depend. Details are listed below.
Claim 1 recites the following in lines 2-3: “enzyme comprising SEQ ID NO: 3 (BdDHS1b).” What is inside the parentheses appears to be a protein/enzyme from a specific plant species. It is unclear whether what is inside the parentheses are intended to be claim limitations. It is also unclear whether SEQ ID NO: 3 and BdDHS1b are intended to be synonymous or whether they encompass disparate scopes. There is a possibility that a sequence bearing a few substitutions could still be considered a BdDHS1b. It is unclear if this is the case due to the use of parenthesis. Similar use of parentheses occur multiple times in claim 1. Claim 2 is similarly rejected for being indefinite due to for multiple instances of a SEQ ID NO followed by species specific protein name within parenthesis (see lines 3-5).
Claim Rejections - 35 USC § 112(d)
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claim 2 is rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 2 depends from claim 1 with the additional limitation that the cell is engineered to express or overexpress both: a) the DHS1b enzyme; and b) a TyrA enzyme selected from the group consisting of SEQ ID NO: 33 (BdTyrA1), SEQ ID NO: 35 (BdTyrA2), SEQ ID NO: 37 (BdTyrAnc), SEQ ID NO: 39 (SbTyrA1), SEQ ID NO: 41 (SbTyrA2), SEQ ID NO: 43 (SbTyrAnc) and an enzyme having at least 95% sequence identity to one of SEQ ID NOs: 33, 35, 37, 39, 41 and 43. Claim 1 recites that “a noncanonical TyrA enzyme comprising SEQ ID NO: 37 (BdTyrAnc), SEQ ID NO: 43 (SbTyrAnc) or a TyrA enzyme having at least 95% identity to SEQ ID NO: 37 or 43.” Claim 2 fails to further limit claim 1’s limitations because the SEQ ID NOs introduced in claim 2 do not have at least 95% identity to either SEQ ID NOs: 37 or 43 (e.g., SEQ ID NO: 33 has less than 50% identity to either of SEQ ID NOs: 37 or 43; data not shown). This means that claim 2 is claiming embodiments which are outside the scope of its parent claim 1. Thus, claim 2 is of improper dependent form.
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1-9 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Panik (U.S. Patent Application Publication No. 20150152431-A1, assigned to Evogene Ltd., titled 'ISOLATED POLYNUCLEOTIDES AND POLYPEPTIDES, AND METHODS OF USING SAME FOR INCREASING NITROGEN USE EFFICIENCY, YIELD, GROWTH RATE, VIGOR, BIOMASS, OIL CONTENT, AND/OR ABIOTIC STRESS TOLERANCE ', published 2015-06-04). Details are listed below.
Regarding claims 1 and 3-6, Panik teaches that “Nitrogen is an essential macronutrient for the plant, responsible for biosynthesis of amino and nucleic acids” (para 0003) and claims “a method of increasing nitrogen use efficiency[(i.e., biosynthesis of amino and nucleic acids; c.f., claim 9)]…of a plant[(c.f., claims 1 and 5-6), comprising expressing within the plant an exogenous[(i.e., not native to the plant cells; c.f., claim 1 line 8)] polynucleotide comprising a nucleic acid sequence encoding a polypeptide at least 80% identical to SEQ ID NO: [4180] thereby increasing the nitrogen use efficiency…of the plant” (emphasis provided; Panik’s claim 1) with further teaching of “stable transformation, [where the] the exogenous polynucleotide is integrated into the plant genome” (c.f., instant claim 4) (Panik para 0295)
Panik’s SEQ ID NO: 4180 is identical to the instant SEQ ID NO: 3 (i.e., instant claim 1’s recitation of a 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase 1b (DHS1b) enzyme comprising SEQ ID NO: 3 (BdDHS1b)) (see alignment below). This also means that Panik’s claim 1 and the recitation of “nucleic acid sequence encoding a polypeptide at least 80% identical to SEQ ID NO: [4180]” therein reads on the instant claim 3’s recitation of “wherein the cell comprises an exogenous nucleic acid encoding the enzyme.” Also, Panik’s SEQ ID NOs: 4173-4174 have at least 95% identity to the instant SEQ ID NO: 27 (data not shown).
US-14-360-960A-4180
(NOTE: this sequence has 3 duplicates in the database searched.
See complete list at the end of this report)
Sequence 4180, US/14360960A
Publication No. US20150152431A1
GENERAL INFORMATION
APPLICANT: Evogene Ltd
APPLICANT: Panik, David
APPLICANT: Vinocur, Judith Basia
APPLICANT: Karchi, Hagai
TITLE OF INVENTION: ISOLATED POLYNUCLEOTIDES AND POLYPEPTIDES, AND METHODS OF USING SAME FOR INCREASING NITROGEN USE EFFICIENCY, YIELD, GROWTH RATE, VIGOR, BIOMASS, OIL CONTENT, AND/OR ABIOTIC STRESS TOLERANCE
FILE REFERENCE: 54577
SEQ ID NO 4180
LENGTH: 542
TYPE: PRT
ORGANISM: Brachypodium distachyon
Query Match 100.0%; Score 2812; Length 542;
Best Local Similarity 100.0%;
Matches 542; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MALATNHAAAAISSGAAAPQPRRAPSFLPLKRRTICAVHAAEPSKSAAAAPAAAKTSSPS 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MALATNHAAAAISSGAAAPQPRRAPSFLPLKRRTICAVHAAEPSKSAAAAPAAAKTSSPS 60
Qy 61 VAPEKSAIPDPKPEAPAVPAKWTVDSWRAKKALQLPEYPNAAELESALKTIEAFPPIVFA 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 VAPEKSAIPDPKPEAPAVPAKWTVDSWRAKKALQLPEYPNAAELESALKTIEAFPPIVFA 120
Qy 121 GEARHLEERLADAAMGRAFLLQGGDCAESFKEFNGNNIRDTFRVLLQMSAVLTFGGQMPV 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 GEARHLEERLADAAMGRAFLLQGGDCAESFKEFNGNNIRDTFRVLLQMSAVLTFGGQMPV 180
Qy 181 IKVGRMAGQFAKPRSDSFEVRDGVKLPSYRGDNINGDAFNEKSRIPDPQRMIRAYTQSAA 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 IKVGRMAGQFAKPRSDSFEVRDGVKLPSYRGDNINGDAFNEKSRIPDPQRMIRAYTQSAA 240
Qy 241 TLNLLRAFAMGGYAAMQRVTQWNLDFTENSEQGDRYRELAHRVDEALGFMSAAGLTLDHP 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 TLNLLRAFAMGGYAAMQRVTQWNLDFTENSEQGDRYRELAHRVDEALGFMSAAGLTLDHP 300
Qy 301 VMSSTEFWTSHECLLLPYEQALTRQDSTSGLFYDCSAHMLWVGERTRQLDGAHVEFLRGV 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 VMSSTEFWTSHECLLLPYEQALTRQDSTSGLFYDCSAHMLWVGERTRQLDGAHVEFLRGV 360
Qy 361 ANPLGIKVSDKMNPADLVKLIDILNPTNKPGRITIITRMGAENMRVKLPHLIRAVRHAGQ 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 361 ANPLGIKVSDKMNPADLVKLIDILNPTNKPGRITIITRMGAENMRVKLPHLIRAVRHAGQ 420
Qy 421 IVTWITDPMHGNTIKAPCGLKTRPFDSILAEVRAFFDVHEQEGSHAGGVHLEMTGQNVTE 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 421 IVTWITDPMHGNTIKAPCGLKTRPFDSILAEVRAFFDVHEQEGSHAGGVHLEMTGQNVTE 480
Qy 481 CIGGSRTVTFDDLGDRYHTHCDPRLNASQSLELSFIIAEKLRKRRIRSSKLNSVLPLPTY 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 481 CIGGSRTVTFDDLGDRYHTHCDPRLNASQSLELSFIIAEKLRKRRIRSSKLNSVLPLPTY 540
Qy 541 GF 542
||
Db 541 GF 542
Regarding claim 2, which depends from claim 1, Panik teaches that “plants include, but not limited to, …Sorghum (Sorghum bicolor)” (para 0469). Cells of the Sorghum bicolor plant would naturally already express a TyrA enzyme selected from the group consisting of …SEQ ID NO: 39 (SbTyrA1), SEQ ID NO: 41 (SbTyrA2), SEQ ID NO: 43 (SbTyrAnc) and an enzyme having at least 95% sequence identity to one of SEQ ID NOs: …39, 41 and 43, absent evidence to the contrary. Therefore, the method of Panik’s claim 1 comprising expressing within the [Sorghum bicolor] plant an exogenous [(i.e., not native to the plant cells; c.f., claim 1 line 8)] polynucleotide comprising a nucleic acid sequence encoding a polypeptide at least [95]% identical to SEQ ID NO: [4180 (i.e., SEQ ID NO: 3 (BdDHS1b)]” produces a cell engineered to express or overexpress both the DHS1b enzyme and a TyrA enzyme selected from the group consisting of …SEQ ID NO: 39 (SbTyrA1), SEQ ID NO: 41 (SbTyrA2), SEQ ID NO: 43 (SbTyrAnc) and an enzyme having at least 95% sequence identity to one of SEQ ID NOs: …39, 41 and 43 where Panik’s SEQ ID NO: 4180 is not native to the Sorghum bicolor plant cells.
Regarding claim 7-8, Panik teaches that “plants include, but not limited to, …Rice (Oryza sativa), [and] …Sorghum (Sorghum bicolor)” (para 0469).
Regarding claim 9, Panik teaches and claims a “polypeptide comprising an amino acid sequence [of] SEQ ID NO: [4180], wherein said amino acid sequence is capable of increasing nitrogen use efficiency… of a plant” (Panik Claim 10) where “as used [t]herein the term ‘increasing’ refers to… increase in fertilizer use efficiency (e.g., nitrogen use efficiency)… of a plant as compared to a native plant or a wild type plant… of the same species [i.e., a control plant] which is grown under the same (e.g., identical) growth conditions” (para 0113).
Absent evidence to the contrary, increasing nitrogen use efficiency includes increasing the quantity of aromatic amino acids produced by the plant compared to a non-transformed plant.
Also, as a matter of scientific principle and established patent law, a gene's structure dictates its function (i.e., structure reads on function). The instantly claimed functional properties and characteristics, are inherently present in Panik’s plant so long as there is expression or overexpression of the enzyme having at least 95% identity to the amino acid sequence of SEQ ID NO: 3 (i.e., Panik’s SEQ ID NO: 4180) as recited by Applicant. Since the Patent Office does not have the facilities to examine and compare the plant of Applicant’s with that of Panik, the burden of proof is upon the Applicant to show an unobvious distinction.
Thus, Panik anticipates the claimed inventions.
Claims 1 and 3-9 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Troukhan (U.S. Patent Application Publication No. US20090094717-A1, assigned to Ceres Inc, titled ' Nucleotide sequences and corresponding polypeptides conferring modulated plant characteristics', published 2009). Details are listed below.
Regarding claim 1, Troukhan teaches and claims in Troukhan’s claim 1 “an isolated nucleic acid molecule comprising…a nucleotide sequence encoding an amino acid sequence that is at least 85% identical to any one of the polypeptides in the Sequence Listing” which includes SEQ ID NO: 6386. SEQ ID NO: 6386 has 100% identity to instant SEQ ID NO: 43 such that SEQ ID NO: 6386 reads on “making plants with altered amino acid content (SbTyrAnc)”) (see snippet below).
RESULT 1
US-12-286-964-6386
(NOTE: this sequence has 2 duplicates in the database searched.
See complete list at the end of this report)
Sequence 6386, US/12286964
Publication No. US20090094717A1
GENERAL INFORMATION
APPLICANT: Maxim Troukhan
APPLICANT: Peter Mascia
TITLE OF INVENTION: NUCLEOTIDE SEQUENCES AND CORRESPONDING POLYPEPTIDES CONFERRING
MODULATED PLANT CHARACTERISTICS
FILE REFERENCE: 2750-1716PUS2
CURRENT APPLICATION NUMBER: US/12/286,964
CURRENT FILING DATE: 2008-12-01
PRIOR APPLICATION NUMBER: 60/997,507
PRIOR FILING DATE:
PRIOR FILING DATE: 2007-10-03
NUMBER OF SEQ ID NOS: 21783
SEQ ID NO 6386
LENGTH: 382
TYPE: PRT
ORGANISM: Sorghum bicolor
FEATURE:
NAME/KEY: misc_feature
OTHER INFORMATION: Ceres ANNOT ID no. 6065871
FEATURE:
NAME/KEY: misc_feature
LOCATION: (31)..(382)
OTHER INFORMATION: NCBI GI: 92884247
NCBI Desc: prephenate dehydrogenase; nadp oxidoreductase,
coenzyme f420-dependent [medicago truncatula]
FEATURE:
NAME/KEY: misc_feature
LOCATION: (37)..(371)
OTHER INFORMATION: SWISSPROT Homolog: EC 1.3.1.78
Arogenate dehydrogenase 2, chloroplast precursor
Query Match 100.0%; Score 1982; Length 382;
Best Local Similarity 100.0%;
Matches 382; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MASSLRHFAGLGCFPAVASTSGSTCCLRRYTPNFCAFVALRPISPPAATATATAKALTSP 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MASSLRHFAGLGCFPAVASTSGSTCCLRRYTPNFCAFVALRPISPPAATATATAKALTSP 60
Qy 61 SPVEQHLQAVVPCHGISDPPAASSAAAVPAAPLRVGIVGFGNFGQFIAGGLQRQGHVVLA 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 SPVEQHLQAVVPCHGISDPPAASSAAAVPAAPLRVGIVGFGNFGQFIAGGLQRQGHVVLA 120
Qy 121 ASRSDYSVYCASHGIRFFRSVDALCEEQPDVLLICSSILSTEGVVRAIPFRKLRHDTIVA 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 ASRSDYSVYCASHGIRFFRSVDALCEEQPDVLLICSSILSTEGVVRAIPFRKLRHDTIVA 180
Qy 181 DVLSVKEFPRNLLLEVLPPGFGIICTHPMFGPESGKHGWGKLPFVFDKVRVAEDGDQAAK 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 DVLSVKEFPRNLLLEVLPPGFGIICTHPMFGPESGKHGWGKLPFVFDKVRVAEDGDQAAK 240
Qy 241 CDQFLSIFEQEGCRMVEMSCAEHDRYAAGSQFITHTIGRVLSQLNLKSTPINTKGYETLL 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 CDQFLSIFEQEGCRMVEMSCAEHDRYAAGSQFITHTIGRVLSQLNLKSTPINTKGYETLL 300
Qy 301 QLTKNTVSDSFDLYYGLFMYNVNATEQLDKLEMAFEKVRQMLSGRLHDFIRKQIVERAAH 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 QLTKNTVSDSFDLYYGLFMYNVNATEQLDKLEMAFEKVRQMLSGRLHDFIRKQIVERAAH 360
Qy 361 VPADPSGKLANGLSSSPAARLL 382
||||||||||||||||||||||
Db 361 VPADPSGKLANGLSSSPAARLL 382
Troukhan teaches in para 0012 that the nucleic acid “molecules may be from the plant itself, and simply expressed at a higher or lower level, or the molecules may be from different plant species [i.e., not native to the plant or cell]” (i.e., a cell engineered to express or overexpress a noncanonical TyrA enzyme compromising SEQ ID NO: 43. (emphasis provided).
Regarding claim 3, Troukhan teaches in para 0023 that “the isolated nucleic acid molecule of the present invention may be exogenous [i.e., exogenous nucleic acid encoding the enzyme] to the plant, plant cell, plant material or seed of a plant.”
Regarding claim 4-6, Troukhan teaches in para 0093 that “Nucleic acid molecules of the present invention may be introduced into the genome or the cell of the appropriate host plant by a variety of techniques”.
Regarding claim 7-8, Troukhan teaches in para 0100 that the “methods of the [Troukhan’s] invention are preferably used in plants that are important or interesting for agriculture, horticulture, biomass for the production of liquid fuel molecules and other chemicals, and/or forestry…,for instance,… Sorghum bicolor (sorghum, sudangrass), …Populus balsamifera (poplar), Zea mays (corn), Glycine max (soybean), Brassica napus (canola), Triticum aestivum (wheat), Gossypium hirsutum (cotton), [and] Oryza sativa (rice).”
Regarding claim 9, Troukhan teaches in para 0120 that “Some nucleotides and polypeptides that are useful for modulating plant characteristics in traits such as the composition of a plant, plant material, plant tissue, plant cell and seed from a plant include those that [are] useful for making plants with altered amino acid content.”
Absent evidence to the contrary, making plants with altered amino acid content includes increasing the quantity of aromatic amino acids produced by the plant compared to a non-transformed plant.
Also, as a matter of scientific principle and established patent law, a gene's structure dictates its function (i.e., structure reads on function). The instantly claimed functional properties and characteristics, are inherently present in Troukhan’s plant so long as there is expression or overexpression of the enzyme having at least 95% identity to the amino acid sequence of SEQ ID NO: 43 (i.e., Troukhan’s SEQ ID NO: 6386) as recited by Applicant. Since the Patent Office does not have the facilities to examine and compare the plant of Applicant’s with that of Troukhan, the burden of proof is upon the Applicant to show an unobvious distinction.
Thus, Troukhan anticipates the claimed inventions.
Double Patenting
Nonstatutory Double Patenting Rejection
The is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the "right to exclude" granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Langi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321 (c) or 1.321 (d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file
provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321 (b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111 (a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 1, 3-7, and 9 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 14, 21, 24, and 27 of copending Application No. 18717257 (i.e., ‘257; See reference application publication US-20250043299-A1). Although the claims at issue are not identical, they are not patentably distinct from each other. Details are listed below.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claim 1 of ‘257 is drawn to an engineered 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (DHS) polypeptide comprising at least one mutation at a position corresponding to amino acid residue 109, 114, 159, 240, 244, 245, 247, 248, 319, 322, or 348 of SEQ ID NO:1 (DHS1), wherein the polypeptide has at least 80% sequence identity to a polypeptide selected from SEQ ID NO:1-37.
SEQ ID NO: 10 of ‘257 is 100% identical to the full length sequence of instant SEQ ID NO: 19 (see alignment below).
[AltContent: textbox (RESULT 1
US-18-717-257-10
Query Match 100.0%; Score 2875; DB 1; Length 555;
Best Local Similarity 100.0%;
Matches 555; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MSLATSSSMAGGAAVVPRSATATTASAFVTMKRRATAVRAVHAAEPSKNPPVGVPSAAKT 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MSLATSSSMAGGAAVVPRSATATTASAFVTMKRRATAVRAVHAAEPSKNPPVGVPSAAKT 60
Qy 61 SSPSVAAPEKAPVAAAPAPVAPAPAATKQVAPARWAVDSWRTKKALQLPEYPNAAELEAV 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 SSPSVAAPEKAPVAAAPAPVAPAPAATKQVAPARWAVDSWRTKKALQLPEYPNAAELEAV 120
Qy 121 LKTIEAFPPIVFAGEARHLEERLADAAMGRAFLLQGGDCAESFKEFNGNNIRDTFRVLLQ 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 LKTIEAFPPIVFAGEARHLEERLADAAMGRAFLLQGGDCAESFKEFNGNNIRDTFRVLLQ 180
Qy 181 MSAVLTFGGQMPVIKVGRMAGQFAKPRSEAFEERDGVKLPSYRGDNINGDAFNEKSRIPD 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 MSAVLTFGGQMPVIKVGRMAGQFAKPRSEAFEERDGVKLPSYRGDNINGDAFNEKSRIPD 240
Qy 241 PQRMVRAYAQSAATLNLLRAFATGGYAAMQRVTQWNLDFTQHSEQGDRYRELAHRVDEAL 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 PQRMVRAYAQSAATLNLLRAFATGGYAAMQRVTQWNLDFTQHSEQGDRYRELAHRVDEAL 300
Qy 301 GFMSAAGLTVDHPLMTSTDFWTSHECLLLPYEQSLTRQDSTTGHFYDCSAHMLWVGERTR 360
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Db 301 GFMSAAGLTVDHPLMTSTDFWTSHECLLLPYEQSLTRQDSTTGHFYDCSAHMLWVGERTR 360
Qy 361 QLDGAHVEFLRGVANPLGIKVSDKMNPTELVKLIEILNPSNKPGRITIITRMGAENMRVK 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 361 QLDGAHVEFLRGVANPLGIKVSDKMNPTELVKLIEILNPSNKPGRITIITRMGAENMRVK 420
Qy 421 LPHLIRAVRHAGQIVTWITDPMHGNTIKAPCGLKTRPFDSILAEVRAFFDVHDQEGSHPG 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 421 LPHLIRAVRHAGQIVTWITDPMHGNTIKAPCGLKTRPFDSILAEVRAFFDVHDQEGSHPG 480
Qy 481 GVHLEMTGQNVTECIGGSRTVTFDDLGDRYHTHCDPRLNASQSLELSFIIAERLRRKRIR 540
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Db 481 GVHLEMTGQNVTECIGGSRTVTFDDLGDRYHTHCDPRLNASQSLELSFIIAERLRRKRIR 540
Qy 541 SSKLNNMLPLPPFGV 555
|||||||||||||||
Db 541 SSKLNNMLPLPPFGV 555)]
Claim 14 of `257 is drawn to a cell comprising the engineered polypeptide of ‘257’s claim 1. This is equivalent to the instant claim 1 which is drawn to a cell engineered to express an DHS1b enzyme comprising SEQ ID NO: 19 (OsDHS1b) or a DHS1b enzyme having at least 95% identity to one of SEQ ID 19; wherein (i) the cell is engineered to express an enzyme that is not native to the cell, or (ii) the cell is engineered to overexpress an enzyme that is native to the cell as compared to a control cell.
Regarding instant claim 3, the engineered polypeptide of ‘257’s claim 1 contains at least one mutation means the polynucleotide encoding the engineered polypeptide is itself engineered and thus is an exogenous nucleic acid. Therefore, the claim 14 of ‘257 also reads on instant claim 3 recitation of wherein the cell encompasses an exogenous nucleic acid.
Alternatively, ‘257’s claim 24 is drawn to a method for increasing production of aromatic amino acids in a plant, the method comprising: introducing the polynucleotide of ‘257’s claim 5 into the plant where ‘257’s claim 5 is drawn to a polynucleotide encoding the engineered polypeptide of ‘257’s claim 1. ‘257’s claim 24 reads on instant claim 3 where the plant produced by method of 257’s claim 24 method is comprised of cells comprising an exogenous nucleic acid encoding the enzyme. ‘257’s claim 24 also reads on instant claim 5 (i.e., the cell is a plant cell), and on instant claim 6 (i.e., a plant comprising of the cell of claim 5).
Regarding instant claim 7 '257’s claim 27 is drawn to the method of '257’s claim 24, wherein the plant is selected from a tomato plant, a tobacco plant, a soybean plant, a cotton plant, a poplar plant, a sorghum plant, a rice plant, and a corn plant. This reads on instant claim 7 which recites “the plant of claim 6, wherein the plant is a tomato plant, tobacco plant, soybean plant, cotton plant, poplar plant, sorghum plant, corn plant, beet plant, mung bean plant, opium poppy plant, alfalfa plant, wheat plant, barley plant, millet plant, oat plant, rye plant, rapeseed plant, miscanthus plant, or grass plant.”
Regarding instant claim 9, '257’s claim 21, which depends from '257’s claim 19, is drawn to a plant comprising the engineered polypeptide of '257’s claim 1, wherein the plant produces a greater quantity of aromatic amino acids as compared to a control plant. This reads on instant claim 9.
Claim 2 is rejected on the ground of nonstatutory double patenting as being unpatentable over claims 7 of Patent (i.e., ‘636; See reference patent publication US-11136559-B2, published 2021-10-05) Although the claims at issue are not identical, they are not patentably distinct from each other. Details are listed below.
This is a nonstatutory double patenting rejection because the patentably indistinct claims have in fact been patented.
'636’s claim 1 is drawn to an “engineered arogenate dehydrogenase polypeptide comprising at least 95% sequence identity to any one of the polypeptides of SEQ ID NOs: 218-242 having a non-acidic amino acid at a position corresponding to residue 220 of SEQ ID NO:10, wherein the engineered mutant arogenate dehydrogenase polypeptide has increased prephenate dehydrogenase activity as compared to an identical sequence with a D or E amino acid at a position corresponding to amino acid residue 220 of SEQ ID NO: 10”(emphasis provided). '636’s SEQ ID NO: 230 is identical to instant SEQ ID NO: 39 (data not shown).
'636’s claim 7 is drawn to a plant cell comprising the engineered polypeptide of '636’s claim 1. Thus '636’s claim 7 reads on instant claim 2 part b recitation of a cell “engineered to express a TyrA enzyme selected from the group consisting of … SEQ ID NO: 39 (SbTyrA).”
Further '636’s claim 9, which depends from '636’s claim 8, is drawn to a “method for increasing production of at least one product of the tyrosine or HPP pathways in a cell comprising introducing the engineered polypeptide of ['636’s] claim 1 into the cell” “wherein the cell is a plant cell.” This also reads on instant claim 2 part b.
Rice, Oryza sativa (Os), is an agronomically and economically important plant while Setaria viridis is a model system for the genetic and molecular characterization of cereals and bioenergy crops like corn and sorghum. After reading '636’s claim 9, one of ordinary skill in the art would be interested in “increasing production of at least one product of the tyrosine or HPP pathways in an Oryza sativa or Setaria viridis plant and be motivated to introduce the engineered polypeptide of '636’s claim 1 into the plant and/or cells thereof. Cells of the Oryza sativa and Setaria viridis plants would, respectively naturally already express a 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase 1b (DHS1b) enzyme comprising SEQ ID NO: 19 (OsDHS1b) or an enzyme having at least 95% identity to SEQ ID NO: 19, and comprising SEQ ID NO: 27 (SvDHS1b) or an enzyme having at least 95% identity to SEQ ID NO: 27, absent evidence to the contrary. Therefore, the method of '636’s claim 9 comprising introducing the engineered polypeptide of ['636’s] claim 1 into the cell produces a cell engineered to express or overexpress both the DHS1b enzyme and a TyrA enzyme selected from the group consisting of …SEQ ID NO: 39 (SbTyrA1), and an enzyme having at least 95% sequence identity to one of SEQ ID NOs: …39, where '636’s SEQ ID NO: 230 (i.e., instant SEQ ID NO: 39) is not native to Oryza sativa or Setaria viridis plant cells. Thus, '636’s claim 9 meet the limitations of instant claim 2.
Note that instant claim 2, which depends from instant claim 1 and has no dependents, is of improper dependent form (see 35 USC § 112d rejection above). As such instant claim 2 is the only rejected claim.
References Cited but not Relied Upon
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
Yokoyama (Ryo Yokoyama, et al., The entry reaction of the plant shikimate pathway is subjected to highly complex metabolite-mediated regulation, The Plant Cell, Volume 33, Issue 3, March 2021, Pages 671–696, https://doi.org/10.1093/plcell/koaa042, published 2021-03, Cited in IDS) Yokoyama teaches that “Actively growing young tissues, for example, have developing plastids with limited photosynthetic activity, but have a high demand for AAAs [i.e., aromatic amino acids], along with other amino acids, to support rapid growth” (Discussion para 2).
Yokoyama also teaches, in figure 1 and caption, that the “shikimate pathway and biosynthesis of AAAs[aromatic amino acids] in plants” includes the enzymes : “1DHS, 3- deoxy-D-arabino-heptulosonate 7-phosphate synthase; EPSPS, 5-enolpyruvylshikimate-3-phosphate synthase; AS, anthranilate synthase; CM, chorismate mutase; TyrA, arogenate dehydrogenase” (i.e., DHS and TyrA enzymes are both part of the AAA biosynthesis pathway)(emphasis provided). Yokoyama specifically teaches type I and type II DHSs where “unlike type I DHSs having a single allosteric effector binding site,” “type II DHSs appear to have more complex regulatory mechanisms than type I enzymes… and are inhibited by the combination of [AAAs, ]Phe and Trp, but not by individual ones” (e.g., “M. tuberculosis type II DHS has at least two effector binding sites for Phe and Trp”) (Introduction, penultimate para). Yokoyama also teaches that “Arabidopsis thaliana has three type II DHS enzymes, AthDHS1, 2, and 3, which are encoded by AT4G39980, AT4G33510, and AT1G22410, respectively” (Introduction, penultimate para) where “Tyr and Trp specifically inhibited AthDHS2, but not AthDHS1 and AthDHS3” (Introduction, ultimate para). Yokoyama then teaches, in figure 10B and caption, a working model of the shikimate pathway and biosynthesis of AAAs in seedling plants which includes an “AAA-inhibited AtDHS2 isoform [which] is dominantly expressed and directly inhibited by Tyr and Trp,” and a Tyr-inhibited TyrA enzyme. This model suggest that Tyr and Trp, AAAs, inhibit the DHS2 production of more AAAs, including Tyr and Trp. The same figure teaches that AthDHS1 and AthDHS3 enzymes, which are not directly inhibited by AAAs are expressed at lower levels (see snippet below). Based on this teaching one of ordinary skill in the art would recognize a benefit to expressing or over expressing DHS1 or DHS2 homolog/orthologs which are not inhibited by AAAs, Tyr and Trp.
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Yokoyama teaches in the Materials and Methods section that “DHS orthologs were… identified by BlastP searches utilizing the amino acid sequence of AthDHS1 as query” (para bridging pages 691-692). Based on these teachings one of ordinary skill in the art wanting to practice in a monocot (e.g., economically important crops like rice, wheat, and corn) would want to find a similar gene from a monocot which would already be codon-optimized for monocot plants. Yokoyama teaches that both DHS and canonical TyrA are inhibited by their AAA products (see snippet above) such that upon discovery of DHS or TyrA that are not inhibited by their downstream products, one of ordinary skill in the art would be motivated to combine the expression of the newly discovered/characterized Shikimate pathway enzymes of Yokoyama’s and Schenck’s into one cell with reasonable expectation of observing increased accumulation of their AAA products in the absence of the negative feedback of said products. BlastP searches utilizing the amino acid sequence of AthDHS1 (NCBI Reference Sequence: NP_173657.1, published by 2015), encoded by AT1G22410, as query reveals phospho-2-dehydro-3-deoxyheptonate aldolase 1, chloroplastic [Brachypodium distachyon] (NCBI Reference Sequence: XP_003557788.1) as the closest homolog in monocot plant, Brachypodium distachyon. NCBI Reference Sequence: XP_003557788.1 (published by 2015), is identical to instant SEQ ID NO: 3 (data not shown).
Lynch (Lynch JH, Dudareva N. Aromatic Amino Acids: A Complex Network Ripe for Future Exploration. Trends Plant Sci. 2020 Jul;25(7):670-681. doi: 10.1016/j.tplants.2020.02.005. Epub 2020 Mar 13. PMID: 32526172, Cited in IDS) abbreviates prephenate dehydrogenase (PDH) and then arogenate dehydrogenase (ADH), and teaches that “analyses revealed that a single amino acid residue (corresponding to Asn222 in Glycine max PDH1) determines ADH versus PDH activity…, likely via stabilization of the transition state.”
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Schenck (Schenck, C., et al. Non-plastidic, tyrosine-insensitive prephenate dehydrogenases from legumes. Nat Chem Biol 11, 52–57. 2015. https://doi.org/10.1038/nchembio.1693, published 2015, Cited in IDS) is also in the field of molecular genetics regarding the Shikimate pathway and teaches the following in the abstract:
“Tyr is generally assumed to be synthesized in the plastids via arogenate dehydrogenase (TyrAa, also known also ADH), which is strictly inhibited by L-Tyr. Using phylogenetic and expression analyses, together with recombinant enzyme and endogenous activity assays, we identified prephenate dehydrogenases (TyrAas, also known as PDHs) from two legumes, Glycine max (soybean) and Medicago truncatula. The identified PDHs were phylogenetically distinct from canonical plant ADH enzymes [i.e., PDHs are noncanonical TyrA], preferred prephenate to arogenate substrate, localized outside of the plastids and were not inhibited by L-Tyr. The results provide molecular evidence for the diversification of primary metabolic Tyr pathway via an alternative cytosolic PDH pathway in plants” (emphasis provided).
In Figure 5a, Schenck teaches, Tyr insensitivity of PDHs, [prephenate dehydrogenase or non-canonical TyrA enzyme], and in Figure 5b, “propose[s] alternative Tyr biosynthetic routes” one of which utilizes PDHs but not ADHs (see snippet above). In Figure 3 and caption, Schenck teaches the “Maximum likelihood phylogeny of soybean candidates together with ADHs and PDHs from plants [including monocots,] Brachypodium distachyon [and]Sorghum bicolor.” Schenck teaches, in the Accession codes section, NCBI reference sequence KM507071 which encodes a GmPDH1 (see snippet top right of above snippet) where the GmPDH1 amino acid sequence is represented by NCBI accession number AIU94222.1 (prephenate dehydrogenase 1 [Glycine max], published 2014). BlastP searches utilizing the amino acid sequence of GmPDH1 (NCBI accession number AIU94222.1) as query reveals phospho-2-dehydro-3-deoxyheptonate aldolase 1, chloroplastic [Brachypodium distachyon] (henceforth NCBI Accession XP_002437117.1; published 2017) as 1 of 3 of the closest orthologs in economically important monocot plant, Sorghum bicolor (see snippet below). NCBI Accession XP_002437117.1 is identical SEQ ID NO: 43 (data not shown).
Lopez (Lopez-Nieves S, et al. Two independently evolved natural mutations additively deregulate TyrA enzymes and boost tyrosine production in planta. Plant J. 2022 Feb;109(4):844-855, Cited in IDS) teaches “two independently evolved natural mutations additively deregulate TyrA enzymes” (Title).
Conclusion
No claims allowed.
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/YVETTE B. TAMUKONG/Examiner, Art Unit 1662
/MATTHEW R KEOGH/Primary Examiner, Art Unit 1663
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