DETAILED CORRESPONDENCE
Status of the Application
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claims 1-13 are pending in the application and are being examined on the merits.
Priority
This application is filed under 35 U.S.C. 120 as a continuation application of U.S. non-provisional application no. 18/455,969, filed August 25, 2023, now abandoned, which is filed under 35 U.S.C. 120 as a continuation application of U.S. non-provisional application no. 17/541,565, filed December 3, 2021, which issued as U.S. Patent No. 11,781,121, which is filed under 35 U.S.C. 121 as a divisional application of U.S. non-provisional application no. 16/345,129, filed April 25, 2019, which issued as U.S. Patent No. 11,225,647, which is filed under 35 U.S.C. 371 as a national stage of international application PCT/EP2017/077439, filed October 26, 2017, which claims foreign priority under 35 U.S.C. 119(a)-(d) to European application no. 16196095.0, filed October 27, 2016. A certified copy of the foreign priority document has been filed in application 17/541,565 on December 10, 2021.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on November 7, 2024 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the IDS has been considered by the examiner.
Specification/Informalities
Applicant is requested to update the status of application 18/455,969 at paragraph [0001] of the specification. According to USPTO records, the 18/455,969 application is now abandoned.
The use of the term “BLAST,” which is a trade name or a mark used in commerce, has been noted in this application at paragraph [0230]. The term should be accompanied by the generic terminology; furthermore the term should be capitalized wherever it appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
Claim Objections
Claims 4, 7, and 9 are objected to because of the following informalities:
Claim 4 is objected to for reciting the conjunction “or” between a) and b) and in the interest of improving claim form and grammar, it is suggested that claim 4 be amended to delete “or” between a) and b) and recite “or” between b) and c).
Claims 7 and 9 are objected to for reciting “the amino acid substitution at position…is with the amino acids” and in the interest of improving claim form and grammar, it is suggested that the plural “acids” be amended to recite the singular “acid.”
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.
Claims 1-13 are rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor regards as the invention.
Claim 1 (claims 2-13 dependent therefrom) is indefinite in the recitation of “an amino acid residue corresponding to any of amino acids at positions 89, 97, or 225” because there is no recited reference sequence for determining the relative amino acid position(s) 89, 97, or 225 in the amino acid sequence of the variant polypeptide. In the interest of compact prosecution, applicant may consider amending the phrase “an amino acid residue corresponding to any of amino acids at positions 89, 97, or 225” to recite “an amino acid residue corresponding to any of amino acids at positions 89, 97, or 225 of SEQ ID NO: 17.”
Claim Rejections – Double Patenting
The nonstatutory double patenting rejection 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 Longi, 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 1-13 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-4 and 7 of U.S. Patent No. 11,781,121 B2 (cited on the attached Form PTO-892). Although the claims at issue are not identical, they are not patentably distinct from each other.
Regarding instant claims 1, 2, and 4, claim 1 of the patent recites a variant polypeptide having geranylgeranyl pyrophosphate synthase activity, wherein the variant polypeptide comprises an amino acid sequence having at least 80% sequence identity with the amino acid sequence of SEQ ID NO: 17, and which, when aligned with the amino acid sequence of SEQ ID NO: 17, comprises a substitution of an amino acid residue corresponding to any of amino acids at positions 89, 97, or 225 with a different amino acid.
Regarding instant claim 3, the claims of the patent do not recite overexpression of said variant in a host cell leads to increased production of steviol and/or steviol glycoside as compared to a host cell which overexpresses a reference polypeptide according to SEQ ID NO: 17. However, since the variant polypeptide recited in claims 1 and 7 of the patent is substantially identical to the variant polypeptide recited in claim 3 of this application, it is presumed that overexpression of the variant polypeptide recited in claims 1 and 7 of the patent in a host cell leads to increased production of steviol and/or steviol glycoside as compared to a host cell which overexpresses a reference polypeptide according to SEQ ID NO: 17. See MPEP 2112.01.I.
Regarding instant claims 5 and 6, claim 2 of the patent recites the substitution at position 89 is selected from the group consisting of G89E, G89D, G89N, and G89Q.
Regarding instant claims 7 and 8, claim 3 of the patent recites the substitution at position 97 is selected from the group consisting of A97V, A97G, A97F, A97Y, A97I, and A97L.
Regarding instant claims 9 and 10, claim 4 of the patent recites the substitution at position 225 is selected from the group consisting of A225N, A225G, A225Q, A225V, A225D, A225E, A225F, and A225Y.
Regarding instant claims 11-13, claim 7 of the patent recites the amino acid sequence of the variant polypeptide has at least 95% sequence identity with the amino acid sequence of SEQ ID NO: 17.
Therefore, claims 1-13 of this application are unpatentable over claims 1-4 and 7 of the patent.
Examiner Comment
The claims are drawn to a variant polypeptide having geranylgeranyl pyrophosphate synthase activity, wherein the variant polypeptide comprises an amino acid sequence having at least 80% sequence identity with the amino acid sequence of SEQ ID NO:17 and which comprises a substitution of an amino acid residue corresponding to any of amino acids at positions 89, 97, or 225, with a different amino acid. According to the instant specification, SEQ ID NO: 17 is the amino acid sequence of a Mucor circinelloides geranylgeranyl pyrophosphate synthase (GGPS) (p. 4, bottom).
The closest prior art of record is considered to be Navarro et al. (Experimental Mycology 19:186-190, 1995; cited on the attached Form PTO-892) and UniProt Database Accession Number A0A162TNG5 (October 5, 2016, 1 page; cited on the IDS filed November 7, 2024).
Navarro et al. teach mutants of Mucor circinelloides with mutations in genes encoding enzymes involved in the carotenoid biosynthetic pathway including geranylgeranyl pyrophosphate synthase (p. 186, column 2, middle). Navarro et al. either alone or in combination with the other prior art of record do not teach or suggest substituting one or more amino acids at positions 89, 97, or 225 of Mucor circinelloides geranylgeranyl pyrophosphate synthase with another amino acid.
UniProt Database Accession Number A0A162TNG5 discloses a geranylgeranyl pyrophosphate synthase polypeptide from Phycomyces blakesleeanus with an amino acid sequence that has 74% sequence identity to SEQ ID NO: 17 and has alanine replaced with serine at position 225 of SEQ ID NO: 17 (see attached Appendix for sequence alignment). UniProt Database Accession Number A0A162TNG5 either alone or in combination with the other prior art of record does not teach or suggest an amino acid sequence having at least 80% sequence identity with the amino acid sequence of SEQ ID NO:17.
In this case, the prior art of record fails to teach or suggest a variant polypeptide having geranylgeranyl pyrophosphate synthase activity, wherein the variant polypeptide comprises an amino acid sequence having at least 80% sequence identity with the amino acid sequence of SEQ ID NO:17 and which comprises a substitution of an amino acid residue corresponding to any of amino acids at positions 89, 97, or 225, with a different amino acid. As such, claims 1-13 are considered to be free of the prior art of record.
Conclusion
Status of the claims:
Claims 1-13 are pending.
Claims 1-13 are rejected.
No claim is in condition for allowance.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to DAVID J STEADMAN whose telephone number is (571)272-0942. The examiner can normally be reached on Monday to Friday, 7:30 AM to 4:00 PM.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, MANJUNATH N. RAO can be reached on 571-272-0939. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/David Steadman/
Primary Examiner, Art Unit 1656
APPENDIX
A0A162TNG5_PHYB8
ID A0A162TNG5_PHYB8 Unreviewed; 299 AA.
AC A0A162TNG5;
DT 06-JUL-2016, integrated into UniProtKB/TrEMBL.
DT 06-JUL-2016, sequence version 1.
DT 22-FEB-2023, entry version 23.
DE SubName: Full=Geranylgeranyl pyrophosphate synthetase {ECO:0000313|EMBL:OAD69872.1};
GN Name=carC {ECO:0000313|EMBL:OAD69872.1};
GN ORFNames=PHYBLDRAFT_33722 {ECO:0000313|EMBL:OAD69872.1};
OS Phycomyces blakesleeanus (strain ATCC 8743b / DSM 1359 / FGSC 10004 / NBRC
OS 33097 / NRRL 1555).
OC Eukaryota; Fungi; Fungi incertae sedis; Mucoromycota; Mucoromycotina;
OC Mucoromycetes; Mucorales; Phycomycetaceae; Phycomyces.
OX NCBI_TaxID=763407 {ECO:0000313|EMBL:OAD69872.1, ECO:0000313|Proteomes:UP000077315};
RN [1] {ECO:0000313|EMBL:OAD69872.1, ECO:0000313|Proteomes:UP000077315}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=NRRL 1555(-) {ECO:0000313|Proteomes:UP000077315};
RG DOE Joint Genome Institute;
RA Corrochano L.M., Kuo A., Marcet-Houben M., Polaino S., Salamov A.,
RA Villalobos J.M., Alvarez M.I., Avalos J., Benito E.P., Benoit I.,
RA Burger G., Camino L.P., Canovas D., Cerda-Olmedo E., Cheng J.-F.,
RA Dominguez A., Elias M., Eslava A.P., Glaser F., Grimwood J., Gutierrez G.,
RA Heitman J., Henrissat B., Iturriaga E.A., Lang B.F., Lavin J.L., Lee S.,
RA Li W., Lindquist E., Lopez-Garcia S., Luque E.M., Marcos A.T., Martin J.,
RA Mccluskey K., Medina H.R., Miralles-Duran A., Miyazaki A., Munoz-Torres E.,
RA Oguiza J.A., Ohm R., Olmedo M., Orejas M., Ortiz-Castellanos L.,
RA Pisabarro A.G., Rodriguez-Romero J., Ruiz-Herrera J., Ruiz-Vazquez R.,
RA Sanz C., Schackwitz W., Schmutz J., Shahriari M., Shelest E.,
RA Silva-Franco F., Soanes D., Syed K., Tagua V.G., Talbot N.J., Thon M.,
RA De Vries R.P., Wiebenga A., Yadav J.S., Braun E.L., Baker S., Garre V.,
RA Horwitz B., Torres-Martinez S., Idnurm A., Herrera-Estrella A.,
RA Gabaldon T., Grigoriev I.V.;
RT "Expansion of signal transduction pathways in fungi by whole-genome
RT duplication.";
RL Submitted (JUN-2015) to the EMBL/GenBank/DDBJ databases.
CC -!- SIMILARITY: Belongs to the FPP/GGPP synthase family.
CC {ECO:0000256|RuleBase:RU004466}.
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DR EMBL; KV440990; OAD69872.1; -; Genomic_DNA.
DR RefSeq; XP_018287912.1; XM_018440018.1.
DR AlphaFoldDB; A0A162TNG5; -.
DR STRING; 763407.A0A162TNG5; -.
DR GeneID; 29000924; -.
DR VEuPathDB; FungiDB:PHYBL_33722; -.
DR OrthoDB; 5770at2759; -.
DR Proteomes; UP000077315; Unassembled WGS sequence.
DR GO; GO:0016740; F:transferase activity; IEA:UniProtKB-KW.
DR GO; GO:0008299; P:isoprenoid biosynthetic process; IEA:InterPro.
DR CDD; cd00685; Trans_IPPS_HT; 1.
DR Gene3D; 1.10.600.10; Farnesyl Diphosphate Synthase; 1.
DR InterPro; IPR008949; Isoprenoid_synthase_dom_sf.
DR InterPro; IPR000092; Polyprenyl_synt.
DR InterPro; IPR033749; Polyprenyl_synt_CS.
DR PANTHER; PTHR12001; GERANYLGERANYL PYROPHOSPHATE SYNTHASE; 1.
DR PANTHER; PTHR12001:SF44; GERANYLGERANYL PYROPHOSPHATE SYNTHASE; 1.
DR Pfam; PF00348; polyprenyl_synt; 1.
DR SFLD; SFLDS00005; Isoprenoid_Synthase_Type_I; 1.
DR SUPFAM; SSF48576; Terpenoid synthases; 1.
DR PROSITE; PS00444; POLYPRENYL_SYNTHASE_2; 1.
PE 3: Inferred from homology;
KW Magnesium {ECO:0000256|ARBA:ARBA00022842};
KW Reference proteome {ECO:0000313|Proteomes:UP000077315};
KW Transferase {ECO:0000256|RuleBase:RU004466}.
SQ SEQUENCE 299 AA; 34051 MW; B5B7BEE6214BD986 CRC64;
Query Match 73.6%; Score 1148; DB 28; Length 299;
Best Local Similarity 74.7%;
Matches 218; Conservative 36; Mismatches 38; Indels 0; Gaps 0;
Qy 2 LNSHNRTEERSTEDIILEPYTYLISQPGKDIRAKLISAFDLWLHVPKDVLCVINKIIGML 61
: : | :: | ::|:|||| ||:||||| :| ||||||:|||:| :| | | |:: ||
Db 1 MTASNEIKKPSFDEILLEPYYYLLSQPGKSVRTKLISAFNLWLNVSEDTLKAITKVVEML 60
Qy 62 HNASLMIDDVQDDSDLRRGVPVAHHIYGVPQTINTANYVIFLALQEVMKLNIPSMMQVCT 121
| |||||||||||| ||| |||||:|||:||:|| |||| |||||:::||| :|: | |
Db 61 HTASLMIDDVQDDSVLRRSVPVAHNIYGIPQSINCANYVYFLALQDILKLNDSTMVTVYT 120
Qy 122 EELINLHRGQGIELYWRDSLTCPTEEEYIDMVNNKTSGLLRLAVRLMQAASESDIDYTPL 181
|||||||:||||||:||||||||||:||||||||||||||||||||||||||| :|||||
Db 121 EELINLHKGQGIELFWRDSLTCPTEQEYIDMVNNKTSGLLRLAVRLMQAASESTVDYTPL 180
Qy 182 VNIIGIHFQVRDDYMNLQSTSYTNNKGFCEDLTEGKFSFPIIHAIRKDPSNRQLLNIISQ 241
||:|||||||||||||||| |: |||||||||||||||||||:|| | |||||||||||
Db 181 VNMIGIHFQVRDDYMNLQSQEYSQNKGFCEDLTEGKFSFPIIHSIRADRSNRQLLNIISQ 240
Qy 242 KPTSIEVKKYALEVIRKAGSFEYVREFLRQKEAESLKEIKRLGGNPLLEKYI 293
|||||||||||||:||: ||||:|: || || | :||:|||||||||| :
Db 241 KPTSIEVKKYALEIIRRTGSFEHVKSFLAAKEIEMQEEIERLGGNPLLEKVV 292
Prosecution Insights