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 .
Claims Status
Claims 1-19 are amended.
Claims 1-20 are pending.
Information Disclosure Statement
The information disclosure statements (IDS) submitted on 11/11/2024 and 08/12/2026 are acknowledged. The submission is in compliance with the provision of 37 CFR 1.97. Accordingly, the information disclosure statements have been considered.
Claim Rejections - 35 USC § 112
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 11, 14 and 16 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.
With regards to claim 11, the claim recites “a construction schematic diagram of the plasmid vectors is as shown in FIGS. 2A-2F or FIGS. 9A-9D. It is unclear how the the recitation of “as shown in FIGS. 2A-2F or FIGS. 9A-9D provide further limitations to the claim and therefore the claim is rendered indefinite.
With regards to claim 14, the claim recites “the polynucleotide in a genome of the recombinant strain”. It is unclear if the claim refers to one genome or multiple genomes in the strain, therefore the claim is rendered indefinite.
With regards to claim 16, the claim recites “in a genome of the recombinant strain”. It is unclear if the claim refers to one genome or multiple genomes in the strain, therefore the claim is rendered indefinite.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1, 3, 4, 6, and 18 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a product of nature without significantly more. The claim(s) recite(s) a nerolidol synthase comprising the domains of Pfam Nos. PF01397 and PF03936 having an activity of the nerolidol synthase (claim 1); the nerolidol synthase according to claim 1 comprising an amino acid sequence having at least 90% sequence identity to the amino acid sequence as shown in SEQ ID NO: 3 (claim 3); a polynucleotide molecule comprising at least one nucleotide sequence encoding the nerolidol synthase according to claim 1 (claim 4); a nucleic acid construct comprising the polynucleotide of molecule of claim 4 (claim 6); a method for producing nerolidol comprising a nerolidol synthase according to claim 1 (claim 18) . This judicial exception is not integrated into a practical application because the additional elements do not contribute any meaningful limitation to the natural product. The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because claim 1 recites a nerolidol synthase comprising the domains of Pfam Nos. PF01397 and PF03936 having an activity of the nerolidol synthase ; claim 3 recites the nerolidol synthase according to claim 1 comprising an amino acid sequence having at least 90% sequence identity to the amino acid sequence as shown in SEQ ID NO: 3; claim 4 recites a polynucleotide molecule comprising at least one nucleotide sequence encoding the nerolidol synthase according to claim 1; claim 6 recites a nucleic acid construct comprising the polynucleotide of molecule of claim 4; and claim 18 recites a method for producing nerolidol comprising a nerolidol synthase according to claim 1. The claims encompass a composition of a polypeptide and polynucleotide that is structurally identical to a natural occurring polypeptide and polynucleotide as evidenced by (1) Su et al. Scientific Reports, Vol. 7:40851; published January 2017; PMID: 28128232; and 2) UniProt Database Entry A0A1S5TFB0_TRIWF; first entry date May 10, 2017, and 3) GenBank entry KU588405.1; February 21, 2017). Su et al. disclose a nerolidol synthase (NES) from Tripterygium wilfordii that is responsible for the biosynthesis of (E)-nerolidol (see Abstract pg. 1). The encompassed polypeptide is also involved in the biosynthesis pathway leading to (E)-nerolidol (see Su et al. Scientific Reports, Vol. 7:40851; published January 2017; PMID: 28128232). Uniprot Database entry A0A1S5TFB0_TRIWF discloses that the nerolidol synthase from Tripterygium wilfordii has an amino acid sequence that has 95.3% sequence identity to SEQ ID NO: 3 of the current instant application (see alignment below) and the annotated domains show that it has both PF01397 and PF03936 domains (See UniProt summary). GenBank entry KU588405.1 discloses the nucleotide sequence.
Query Match 95.3%; Score 2635; Length 528;
Best Local Similarity 95.8%;
Matches 506; Conservative 6; Mismatches 16; Indels 0; Gaps 0;
Qy 1 MTISVTRKDTQPTPFPSETDIVSNDINIKNELSIRHLELLEEVRNLLKNCSSKPLVMVDT 60
||||||||||||||||||||||||||:|||||||||||||||||||||| ||||| |||
Db 1 MTISVTRKDTQPTPFPSETDIVSNDIDIKNELSIRHLELLEEVRNLLKNYSSKPLDMVDA 60
Qy 61 LQKLCINHHYEEEIGLILKSLYTRMSNNDDYKHDKSLYEVSLSFRILRQHGYYVSADVFA 120
|||||||||||||||||||||||:| ||||||||||||||||||||||| ||||||||||
Db 61 LQKLCINHHYEEEIGLILKSLYTKMLNNDDYKHDKSLYEVSLSFRILRQEGYYVSADVFA 120
Qy 121 NFKQKDGKFKGEITQDLKGLIALYEASQLSLEGEQILKEASDFSSGALKEMMPSLDQDQA 180
||||||||| |||||||||||||||| ||:||||||||||||||||||||:||||||||
Db 121 NFKQKDGKFDQEITQDLKGLIALYEASHLSMEGEQILKEASDFSSGALKEMVPSLDQDQA 180
Qy 181 MIVTNTLQHTYQRTTSTFMVKKFMKVYTGTPMCELAQLELTKVQSLHRTEVDQISRWWKG 240
|| |||||||||||:|||||||||||| |||| |||||||||||||||||||||||||||
Db 181 MIATNTLQHTYQRTSSTFMVKKFMKVYKGTPMWELAQLELTKVQSLHRTEVDQISRWWKG 240
Qy 241 LGLAQELKLARNQPLHWYLWPMASLTDLSLSEQRVELTKPIAFIFLIDDIFDVYGTLDQL 300
|||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||
Db 241 LGLAQELKLARNQPLHWYLWPMASLTDLSLSEQRVELTKPIAIIFLIDDIFDVYGTLDQL 300
Qy 301 VILTQAVNRWESNRLEQLPYHLRICIQALFDVTNEISDKIYKKHGFNPIEFLKQSWINLC 360
||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||
Db 301 VILTQAVNRWESNCLEQLPYHLRICIQALFDVTNEISDKIYKKHGFNPIEFLKQSWINLC 360
Qy 361 DAFLVEAKWFAEGYMPTAEDYLNNGMVSTGVHVVIVHMFFLLGGGPNIKSASVVNENQGI 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 361 DAFLVEAKWFAEGYMPTAEDYLNNGMVSTGVHVVIVHMFFLLGGGPNIKSASVVNENQGI 420
Qy 421 MSCLAKILRLWDDLGSAKDVDQDGNDGSYVTYYMKENAGCSIQKAHEHVMEMISNTWKQL 480
|||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||
Db 421 TSCLAKILRLWDDLGSAKDVDQDGNDGSYVTYYMKENAGCSSQKAHEHVMEMISNTWKQL 480
Qy 481 NAECLYSSHFSRTFTKACLNLAKMIPMMYDYDENHSLPFIEEYINSMF 528
||||||||||| ||||||||||:|||||||||||||||||||||||||
Db 481 NAECLYSSHFSPTFTKACLNLARMIPMMYDYDENHSLPFIEEYINSMF 528
Because there is no difference in characteristics (structural, functional, or otherwise) between the claimed and naturally occurring composition and function of the composition, the claimed compositions and function (method) do not have markedly different characteristics and thus is a product of nature exception. Accordingly, the product is directed to an exception (Step 2A: Yes). Because the claims do not include any additional features that could add significantly more to the exception (Step 2: No), the claims do not qualify as eligible subject matter and are rejected.
Claims 1, 2, 3, 4, 5, 6, 18 and 20 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a product of nature without significantly more. The claim(s) recite(s) a nerolidol synthase comprising domains of Pfam Nos. PF01397 and PF03936 and having activity of the nerolidol synthase (claim 1); the nerolidol synthase according to claim 1 wherein the nerolidol synthase is derived from Artemisia argyi (claim 2); the nerolidol synthase according to claim 1 comprising an amino acid sequence having at least 90% sequence identity to the amino acid sequence as shown in SEQ ID NO: 3 (claim 3); a polynucleotide molecule comprising at least one of sequences encoding the nerolidol synthase according to claim 3 (claim 4); the polynucleotide molecule according to claim 4, comprising a nucleotide sequence having at least 90% sequence identity to the nucleotide sequence of SEQ ID NO: 7 (claim 5); a nucleic acid construct comprising the polynucleotide according to claim 4 (claim 6); a method for producing nerolidol, comprising using the nerolidol synthase according to claim 1 (claim 18); and the polynucleotide molecule according to claim 4 wherein the nerolidol synthase is derived from Artemisia argyi (claim 20). This judicial exception is not integrated into a practical application because the additional elements do not contribute any meaningful limitation to the natural product.. The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because claim 1 recites a nerolidol synthase comprising domains of Pfam Nos. PF01397 and PF03936 and having activity of the nerolidol synthase; claim 2 recites the nerolidol synthase according to claim 1 wherein the nerolidol synthase is derived from Artemisia argyi; claim 3 recites the nerolidol synthase according to claim 1 comprising an amino acid sequence having at least 90% sequence identity to the amino acid sequence as shown in SEQ ID NO: 3; claim 4 recites a polynucleotide molecule comprising at least one of sequences encoding the nerolidol synthase according to claim 3; claim 5 recites the polynucleotide molecule according to claim 4, comprising a nucleotide sequence having at least 90% sequence identity to the nucleotide sequence of SEQ ID NO: 7; claim 6 recites a nucleic acid construct comprising the polynucleotide according to claim 4; claim18 recites a method for producing nerolidol, comprising using the nerolidol synthase according to claim 1; and claim 20 recites the polynucleotide molecule according to claim 4 wherein the nerolidol synthase is derived from Artemisia argyi . The claims encompass a composition of a polypeptide and polynucleotide that are structurally identical to a natural occurring polypeptide and polynucleotide as evidenced by 1) GenBank entry WWW52537.1; published March 2, 2024, 2) GenBank entry: (PP093022.1; published March 2, 2024), and 3) Li et al. (International Journal of Molecular Sciences, Vol. 26:2113; published 2025). GenBank entry WWW52537.1 discloses a terpene synthase (Artemisia argyi) that shares 100% sequence identity with SEQ ID NO: 3 of the current instant application (see sequence alignment below). GenBank entry PP093022.1 discloses the nucleotide sequence which has 100% sequence identity to SEQ ID NO: 7 of the current instant application (see sequence alignment below) and Li et al. disclose that the protein sequence of terpene synthases is characterized by two domains: the N-terminal domain (Pfam ID PF01397) and the C-terminal domain (Pfam ID PF03936) and that in plants, terpene synthases orchestrate terpenoid biosynthesis. (see pg. 1-2).
RESULT 1
AASEQ2_08132026_155638
Query Match 100.0%; Score 2766; DB 1; Length 528;
Best Local Similarity 100.0%;
Matches 528; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MTISVTRKDTQPTPFPSETDIVSNDINIKNELSIRHLELLEEVRNLLKNCSSKPLVMVDT 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MTISVTRKDTQPTPFPSETDIVSNDINIKNELSIRHLELLEEVRNLLKNCSSKPLVMVDT 60
Qy 61 LQKLCINHHYEEEIGLILKSLYTRMSNNDDYKHDKSLYEVSLSFRILRQHGYYVSADVFA 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 LQKLCINHHYEEEIGLILKSLYTRMSNNDDYKHDKSLYEVSLSFRILRQHGYYVSADVFA 120
Qy 121 NFKQKDGKFKGEITQDLKGLIALYEASQLSLEGEQILKEASDFSSGALKEMMPSLDQDQA 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 NFKQKDGKFKGEITQDLKGLIALYEASQLSLEGEQILKEASDFSSGALKEMMPSLDQDQA 180
Qy 181 MIVTNTLQHTYQRTTSTFMVKKFMKVYTGTPMCELAQLELTKVQSLHRTEVDQISRWWKG 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 MIVTNTLQHTYQRTTSTFMVKKFMKVYTGTPMCELAQLELTKVQSLHRTEVDQISRWWKG 240
Qy 241 LGLAQELKLARNQPLHWYLWPMASLTDLSLSEQRVELTKPIAFIFLIDDIFDVYGTLDQL 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 LGLAQELKLARNQPLHWYLWPMASLTDLSLSEQRVELTKPIAFIFLIDDIFDVYGTLDQL 300
Qy 301 VILTQAVNRWESNRLEQLPYHLRICIQALFDVTNEISDKIYKKHGFNPIEFLKQSWINLC 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 VILTQAVNRWESNRLEQLPYHLRICIQALFDVTNEISDKIYKKHGFNPIEFLKQSWINLC 360
Qy 361 DAFLVEAKWFAEGYMPTAEDYLNNGMVSTGVHVVIVHMFFLLGGGPNIKSASVVNENQGI 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 361 DAFLVEAKWFAEGYMPTAEDYLNNGMVSTGVHVVIVHMFFLLGGGPNIKSASVVNENQGI 420
Qy 421 MSCLAKILRLWDDLGSAKDVDQDGNDGSYVTYYMKENAGCSIQKAHEHVMEMISNTWKQL 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 421 MSCLAKILRLWDDLGSAKDVDQDGNDGSYVTYYMKENAGCSIQKAHEHVMEMISNTWKQL 480
Qy 481 NAECLYSSHFSRTFTKACLNLAKMIPMMYDYDENHSLPFIEEYINSMF 528
||||||||||||||||||||||||||||||||||||||||||||||||
Db 481 NAECLYSSHFSRTFTKACLNLAKMIPMMYDYDENHSLPFIEEYINSMF 528
Query Match 100.0%; Score 1587; Length 1587;
Best Local Similarity 100.0%;
Matches 1587; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 ATGACAATCTCTGTTACTAGAAAGGATACTCAACCAACACCATTTCCATCTGAAACTGAT 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 ATGACAATCTCTGTTACTAGAAAGGATACTCAACCAACACCATTTCCATCTGAAACTGAT 60
Qy 61 ATTGTTTCTAACGATATCAACATCAAGAACGAATTGTCTATTAGACATTTGGAATTGTTG 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 ATTGTTTCTAACGATATCAACATCAAGAACGAATTGTCTATTAGACATTTGGAATTGTTG 120
Qy 121 GAAGAAGTTAGAAATTTGTTGAAGAACTGTTCTTCTAAGCCATTAGTTATGGTTGATACT 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 GAAGAAGTTAGAAATTTGTTGAAGAACTGTTCTTCTAAGCCATTAGTTATGGTTGATACT 180
Qy 181 TTACAAAAGCTGTGTATTAACCATCATTACGAAGAAGAAATCGGTTTGATTTTGAAATCT 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 TTACAAAAGCTGTGTATTAACCATCATTACGAAGAAGAAATCGGTTTGATTTTGAAATCT 240
Qy 241 TTGTACACAAGAATGTCCAATAACGATGATTATAAGCATGATAAGTCCTTATACGAAGTT 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 TTGTACACAAGAATGTCCAATAACGATGATTATAAGCATGATAAGTCCTTATACGAAGTT 300
Qy 301 TCTTTGTCTTTTAGAATCTTGAGACAACATGGTTATTACGTTTCTGCTGATGTTTTTGCT 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 TCTTTGTCTTTTAGAATCTTGAGACAACATGGTTATTACGTTTCTGCTGATGTTTTTGCT 360
Qy 361 AATTTTAAGCAAAAGGACGGTAAATTTAAGGGTGAAATTACACAAGATCTGAAAGGTTTA 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 361 AATTTTAAGCAAAAGGACGGTAAATTTAAGGGTGAAATTACACAAGATCTGAAAGGTTTA 420
Qy 421 ATCGCTTTATATGAAGCTAGTCAATTGTCTTTGGAAGGTGAACAAATTTTAAAGGAAGCT 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 421 ATCGCTTTATATGAAGCTAGTCAATTGTCTTTGGAAGGTGAACAAATTTTAAAGGAAGCT 480
Qy 481 AGTGATTTCTCTTCTGGTGCTTTGAAAGAAATGATGCCATCTTTGGATCAAGATCAAGCT 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 481 AGTGATTTCTCTTCTGGTGCTTTGAAAGAAATGATGCCATCTTTGGATCAAGATCAAGCT 540
Qy 541 ATGATTGTTACAAATACTTTGCAACATACCTACCAAAGAACAACTTCTACTTTTATGGTT 600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 541 ATGATTGTTACAAATACTTTGCAACATACCTACCAAAGAACAACTTCTACTTTTATGGTT 600
Qy 601 AAGAAGTTCATGAAGGTTTACACTGGTACACCAATGTGTGAATTGGCTCAATTGGAATTG 660
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 601 AAGAAGTTCATGAAGGTTTACACTGGTACACCAATGTGTGAATTGGCTCAATTGGAATTG 660
Qy 661 ACTAAAGTTCAATCTTTGCATAGAACAGAAGTTGATCAAATTTCTAGATGGTGGAAAGGT 720
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 661 ACTAAAGTTCAATCTTTGCATAGAACAGAAGTTGATCAAATTTCTAGATGGTGGAAAGGT 720
Qy 721 TTAGGTTTGGCTCAAGAATTAAAATTAGCTAGAAACCAACCATTGCATTGGTATTTATGG 780
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 721 TTAGGTTTGGCTCAAGAATTAAAATTAGCTAGAAACCAACCATTGCATTGGTATTTATGG 780
Qy 781 CCAATGGCTTCTTTGACTGATTTGTCTTTGTCTGAACAAAGAGTTGAATTGACTAAGCCA 840
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 781 CCAATGGCTTCTTTGACTGATTTGTCTTTGTCTGAACAAAGAGTTGAATTGACTAAGCCA 840
Qy 841 ATTGCTTTTATTTTCTTGATCGATGATATCTTCGACGTTTATGGTACTTTGGATCAATTA 900
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 841 ATTGCTTTTATTTTCTTGATCGATGATATCTTCGACGTTTATGGTACTTTGGATCAATTA 900
Qy 901 GTTATCTTGACTCAAGCTGTTAATAGATGGGAATCTAATAGATTAGAGCAATTACCATAC 960
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 901 GTTATCTTGACTCAAGCTGTTAATAGATGGGAATCTAATAGATTAGAGCAATTACCATAC 960
Qy 961 CATTTGAGAATTTGTATCCAAGCTCTATTTGATGTTACAAATGAAATCTCTGACAAGATT 1020
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 961 CATTTGAGAATTTGTATCCAAGCTCTATTTGATGTTACAAATGAAATCTCTGACAAGATT 1020
Qy 1021 TACAAGAAGCATGGTTTTAATCCAATCGAATTTTTGAAGCAATCCTGGATTAATTTGTGT 1080
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1021 TACAAGAAGCATGGTTTTAATCCAATCGAATTTTTGAAGCAATCCTGGATTAATTTGTGT 1080
Qy 1081 GATGCTTTTTTGGTTGAGGCTAAATGGTTTGCTGAAGGTTATATGCCAACTGCTGAAGAT 1140
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1081 GATGCTTTTTTGGTTGAGGCTAAATGGTTTGCTGAAGGTTATATGCCAACTGCTGAAGAT 1140
Qy 1141 TATTTAAACAATGGTATGGTTTCCACAGGTGTTCATGTTGTTATTGTTCATATGTTTTTC 1200
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1141 TATTTAAACAATGGTATGGTTTCCACAGGTGTTCATGTTGTTATTGTTCATATGTTTTTC 1200
Qy 1201 CTGTTGGGTGGTGGTCCAAATATTAAATCTGCTTCTGTTGTTAACGAGAATCAAGGTATT 1260
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1201 CTGTTGGGTGGTGGTCCAAATATTAAATCTGCTTCTGTTGTTAACGAGAATCAAGGTATT 1260
Qy 1261 ATGTCTTGTTTGGCTAAAATTTTGAGGTTATGGGATGATTTAGGTTCTGCTAAAGATGTT 1320
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1261 ATGTCTTGTTTGGCTAAAATTTTGAGGTTATGGGATGATTTAGGTTCTGCTAAAGATGTT 1320
Qy 1321 GATCAAGATGGTAATGATGGTTCTTATGTTACATATTACATGAAGGAAAACGCTGGTTGT 1380
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1321 GATCAAGATGGTAATGATGGTTCTTATGTTACATATTACATGAAGGAAAACGCTGGTTGT 1380
Qy 1381 TCTATTCAAAAAGCTCATGAACATGTTATGGAAATGATTTCTAACACTTGGAAACAATTG 1440
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1381 TCTATTCAAAAAGCTCATGAACATGTTATGGAAATGATTTCTAACACTTGGAAACAATTG 1440
Qy 1441 AACGCTGAATGTTTATATTCCTCTCATTTTTCTAGGACATTCACTAAAGCATGTTTGAAT 1500
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1441 AACGCTGAATGTTTATATTCCTCTCATTTTTCTAGGACATTCACTAAAGCATGTTTGAAT 1500
Qy 1501 TTGGCTAAAATGATCCCAATGATGTATGATTATGACGAAAATCATTCCTTGCCATTTATT 1560
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1501 TTGGCTAAAATGATCCCAATGATGTATGATTATGACGAAAATCATTCCTTGCCATTTATT 1560
Qy 1561 GAAGAATACATTAACTCCATGTTCTAA 1587
|||||||||||||||||||||||||||
Db 1561 GAAGAATACATTAACTCCATGTTCTAA 1587
Because there is no difference in characteristics (structural, functional, or otherwise) between the claimed and naturally occurring composition and function of the composition, the claimed compositions and function (method) do not have markedly different characteristics and thus is a product of nature exception. Accordingly, the product is directed to an exception (Step 2A: Yes). Because the claims do not include any additional features that could add significantly more to the exception (Step 2: No), the claims do not qualify as eligible subject matter and are rejected.
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, 3-4, 6, 8-9, 12-13, 15 and 17-19 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Su et al. (Scientific Reports, Vol. 7:40851; published January 2017; PMID: 28128232), hereinafter referred to as Su.
With regards to claim 1, 3-4, 6, 8-9, 12-13, and 18, Su discloses a gene (nucleic acid construct) encoding a nerolidol synthase (NES, TwNES) that is involved in biosynthesis of (E)-nerolidol (see Abstract, pg. 1). Su discloses that the full-length TwJNES cDNA (GenBank accession number KU588405) is 1891 nt and encodes a polypeptide of 552 amino acids (see pg. 2). As evidenced by UniProt Databank entry: A0A1S5TFB0_TRIWF; first entry date: May 10, 2017), the annotation of the domains of the nerolidol synthase from Tripterygium wilfordii comprises the domains of Pfam Nos. PF01397 and PF03936). The nerolidol synthase disclosed by Su shares 95.3% amino acid sequence identity with SEQ ID NO. 3 of the current instant application (see alignment below).
Query Match 95.3%; Score 2635; Length 528;
Best Local Similarity 95.8%;
Matches 506; Conservative 6; Mismatches 16; Indels 0; Gaps 0;
Qy 1 MTISVTRKDTQPTPFPSETDIVSNDINIKNELSIRHLELLEEVRNLLKNCSSKPLVMVDT 60
||||||||||||||||||||||||||:|||||||||||||||||||||| ||||| |||
Db 1 MTISVTRKDTQPTPFPSETDIVSNDIDIKNELSIRHLELLEEVRNLLKNYSSKPLDMVDA 60
Qy 61 LQKLCINHHYEEEIGLILKSLYTRMSNNDDYKHDKSLYEVSLSFRILRQHGYYVSADVFA 120
|||||||||||||||||||||||:| ||||||||||||||||||||||| ||||||||||
Db 61 LQKLCINHHYEEEIGLILKSLYTKMLNNDDYKHDKSLYEVSLSFRILRQEGYYVSADVFA 120
Qy 121 NFKQKDGKFKGEITQDLKGLIALYEASQLSLEGEQILKEASDFSSGALKEMMPSLDQDQA 180
||||||||| |||||||||||||||| ||:||||||||||||||||||||:||||||||
Db 121 NFKQKDGKFDQEITQDLKGLIALYEASHLSMEGEQILKEASDFSSGALKEMVPSLDQDQA 180
Qy 181 MIVTNTLQHTYQRTTSTFMVKKFMKVYTGTPMCELAQLELTKVQSLHRTEVDQISRWWKG 240
|| |||||||||||:|||||||||||| |||| |||||||||||||||||||||||||||
Db 181 MIATNTLQHTYQRTSSTFMVKKFMKVYKGTPMWELAQLELTKVQSLHRTEVDQISRWWKG 240
Qy 241 LGLAQELKLARNQPLHWYLWPMASLTDLSLSEQRVELTKPIAFIFLIDDIFDVYGTLDQL 300
|||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||
Db 241 LGLAQELKLARNQPLHWYLWPMASLTDLSLSEQRVELTKPIAIIFLIDDIFDVYGTLDQL 300
Qy 301 VILTQAVNRWESNRLEQLPYHLRICIQALFDVTNEISDKIYKKHGFNPIEFLKQSWINLC 360
||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||
Db 301 VILTQAVNRWESNCLEQLPYHLRICIQALFDVTNEISDKIYKKHGFNPIEFLKQSWINLC 360
Qy 361 DAFLVEAKWFAEGYMPTAEDYLNNGMVSTGVHVVIVHMFFLLGGGPNIKSASVVNENQGI 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 361 DAFLVEAKWFAEGYMPTAEDYLNNGMVSTGVHVVIVHMFFLLGGGPNIKSASVVNENQGI 420
Qy 421 MSCLAKILRLWDDLGSAKDVDQDGNDGSYVTYYMKENAGCSIQKAHEHVMEMISNTWKQL 480
|||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||
Db 421 TSCLAKILRLWDDLGSAKDVDQDGNDGSYVTYYMKENAGCSSQKAHEHVMEMISNTWKQL 480
Qy 481 NAECLYSSHFSRTFTKACLNLAKMIPMMYDYDENHSLPFIEEYINSMF 528
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Db 481 NAECLYSSHFSPTFTKACLNLARMIPMMYDYDENHSLPFIEEYINSMF 528
With regards to claims 8-9 and 12-13, 15, 17 and 18, Su discloses that for expression in E. coli (host cell) the open reading frame of NES was subcloned directly into a pMAL-c2X expression vector (see Recombinant expression and affinity purification, pg. 7). As evidenced by NovoPro pMAL-c2X data sheet (cited in PTO-892), the pMAL0-c2X comprises insertion elements to allow for integrating a nucleotide sequence of the gene of interest. Claim 15 is included in the rejection as the E. coli host cell has the inherency of being configured for endogenously expressing at least one of acetoacetyl coenzyme A thiolase, hydroxy-methylglutaryl-coA synthase, hydroxy-methylglutaryl-CoA reductase, mevalonate kinase, mevalonate-5-phosphate kinase, mevalonate pyrophosphate decarboxylase, isoprene pyrophosphate isomerase, and farnesyl pyrophosphate synthase via the pMAL0-c2X expression vector. Claim 17 is included in the rejection due to the recitation of “or knockout of at least one of genes encoding FPP hydrolase DPP1, FPP hydrolase LPP1, citrate synthase, malate synthase, or squalene synthase. The term “knockout” is interpreted as the gene(s) not being present in the nucleic acid construct.
With regards to claims 18-19, Su discloses that the purified protein from E. coli, was added to a mixture of purified proteins in an assay buffer with 25 mM prenyl diphosphate substrates (E,E)-FPP or GGPP). GC-MS analysis was performed to calculate the contents of the product for (E)-nerolidol (see enzymatic assays, pg. 7).
Therefore, claim(s) 1, 3-4, 6, 8-9, 12-13, 15 and 17-19 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Su et al. (Scientific Reports, Vol. 7:40851; published January 2017; PMID: 28128232).
Claim Rejections - 35 USC § 103
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 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
Claims 1-2, 4 and 20 are rejected under 35 U.S.C. 103 as being unpatentable over Khan et al. (BMC Genomics, Vol. 18:54; published 2017), hereinafter referred to as Khan, in view of Yamashiro et al. (Scientific Reports, Vol. 9:18249; published 2019), hereinafter referred to as Yamashiro, and further in view of Zhang et al. (BMC Plant Biology, Vol. 19: 115; published 2019), hereinafter referred to as Zhang.
With regards to claims 1-2, 4 and 20, Khan teaches that the specific transcriptome analysis of the plant T. cinerariifolium resulted in a total of 23,200,000 and 28,500,110 high quality Illumina next generation sequence reads (see Abstract, pg. 1). Khan further teaches that functional enrichment analysis and GO based annotation using public protein databases such as PFAM were conducted (see Abstract, pg. 1).
Khan does not specifically teach the identification of a nerolidol synthase comprising domains of Pfam Nos. PF01397 and PF03936 and having nerolidol synthase activity.
Yamashiro teaches the 7.1Gb draft genome of T. cinerariifolium consisting of 2,016,451 scaffolds and 60,080 genes predicted with high confidence (see Abstract, pg. 1). Yamashiro does not specifically teach the identification of a nerolidol synthase comprising domains of Pfam Nos. PF01397 and PF03936 and having nerolidol synthase activity.
However, Zhang teaches that more than 40 terpene synthase (TPS) unigenes were identified by mining publicly-available RNA-seq data from Santalum album (see Abstract, pg. 1). Zhang further teaches that the TPS N-terminal domain (PF01397) and the TPS family metal binding domain (PF03936) were downloaded from the Pfam database and used as bait to search against the S. album transcriptome with an E-value threshold of 10-5 (see pg. 15). Zhang further teaches the characterization of the identified genes by heterologous expression and purification of the recombinant protein and further analysis by in vitro enzyme assay top confirm terpene biosynthesis activity (see pg. 15).
It would have been obvious to one of ordinary skill in the art of protein engineering before the effective filing date of the current instant application to take the teachings of Zhang and search the T. cinerariifolium transcriptome taught by Khan or the genome sequences taught by Yamashiro by using PF01397 and PF03936 domains as bait to identify nerolidol gene candidates and further characterizing the gene candidates by enzyme assay to confirm biochemical activity as taught by Khan. One of ordinary skill in the art would be motivated to do so in order to identify and characterize a new gene from T. cinerariifolium that has nerolidol synthase activity in order to find a new enzyme that could be used for the biosynthesis of nerolidol. One of ordinary skill in the art would have expectations of success in doing so from the combined teachings of Khan and Zhang who provide all the teachings and methods needed to do so.
Therefore, claims 1-2, 4 and 20 are rejected under 35 U.S.C. 103 as being unpatentable over Khan et al. (BMC Genomics, Vol. 18:54; published 2017) in view of Yamashiro et al. (Scientific Reports, Vol. 9:18249; published 2019) and further in view of Zhang et al. (BMC Plant Biology, Vol. 19: 115; published 2019).
Claim 7 is rejected under 35 U.S.C. 103 as being unpatentable over Su et al. (Scientific Reports, Vol. 7:40851; published January 2017; PMID: 28128232), hereinafter referred to as Su, as applied to claim 6 above, and further in view of Nowroozi et al. (Biotechnology Products and Process Engineering, Vol. 98, pg. 1567-1581; published online November 21, 2013), hereinafter referred to as Nowroozi.
The teachings of Su as applied to claim 6 are summarized above.
Su does not each that the nucleic acid construct comprising the polynucleotide molecules encoding a nerolidol synthase further comprises at least one of the nucleotide sequences encoding acetoacetyl coenzyme A thiolase, hydroxy-methylglutaryl coenzyme A synthase, hydroxy-methylglutaryl coenzyme A reductase, mevalonate kinase, mevalonate-5-phospahte kinase, mevalonate pyrophosphate decarboxylase, isoprene pyrophosphate isomerase, and farnesyl pyrophosphate synthase.
However, Nowroozi teaches that the genes encoding the mevalonate-based farnesyl pyrophosphate (FPP) biosynthetic pathway, were encoded in two operons and expressed in E. coli to increase the production of sesquiterpenes (terpene). Nowroozi teaches that the pMBIS harbors genes for the mevalonate pathway from mevalonate to farnesyl pyrophosphate (FPP) (see pg 1568). The MBIS operon (mevK (mevalonate kinase), pmk, pmd (mevalonate pyrophosphate decarboxylase), idi, and ispA (farnesyl pyrophosphate synthase) was cloned into pBBR1MCS, a low copy plasmid with an IPTG inducible lac promoter to create pMBIS. Nowroozi teaches that the MBIS operons were cloned into a pTrc99a derivate to create a pTRc-M.ADS-MBIS1-9. (ADS is the amorphadiene synthase gene, a terpene synthase). Nowroozi teaches that E. coli DH1 was transformed with the plasmid and cultures were grown (see pg. 1571).
It would have been obvious to one of ordinary skill in the art of protein engineering before the effective date of the current instant application to modify the nucleic construct taught by Su to further comprise an operon containing mevalonate kinase, mevalonate pyrophosphate decarboxylase, and farnesyl pyrophosphate synthase, as taught by Nowroozi in order to increase the production of the terpene, nerolidol. One of ordinary skill in the art would be motivated to do so since, Nowroozi teaches that the MBIS operon which comprises mevalonate kinase, mevalonate pyrophosphate decarboxylase, and farnesyl pyrophosphate synthase, may be used to improve production of the product formed by the terpene synthase, ADS. As nerolidol synthase also depends on the mevalonate-based farnesyl pyrophosphate biosynthetic pathway, one of ordinary skill in the art would be motivated to incorporate the operon into the nucleic acid construct comprising nerolidol synthase to achieve improved production of nerolidol. One of ordinary skill in the art would have expectations of success in doing so from the combined teachings of Su and Nowroozi.
Therefore, claim 7 is rejected under 35 U.S.C. 103 as being unpatentable over Su et al. (Scientific Reports, Vol. 7:40851; published January 2017; PMID: 28128232) as applied to claim 6 above, and further in view of Nowrooozi et al. (Biotechnology Products and Process Engineering, Vol. 98, pg. 1567-1581; published online November 21, 2013).
Claim 10 is rejected under 35 U.S.C. 103 as being unpatentable over Su et al. (Scientific Reports, Vol. 7:40851; published January 2017; PMID: 28128232), hereinafter referred to as Su, as applied to claim 9 above, and further in view of Sun et al. (Biotechnology and Bioengineering, Vol. 109, pg. 2082-2092, published August 2012), hereinafter referred to as Sun.
The teachings of Su as applied to claim 9 are summarized above.
Su does not teach that the nucleic acid construct is a plasmid vector further comprising a pRS426 plasmid backbone.
However, Sun teaches that Saccharomyces cerevisiae is an important platform organism for synthesis of chemicals and fuels. Sun teaches that constitutive promoters from S. cerevisiae were cloned and characterized using a green fluorescent protein as a reporter in vector pRS426 and the strengths of these promoters were measured (see Abstract, pg. 2982).
It would have been obvious to one of ordinary skill in the art of protein engineering before the effective filing date of the current instant application to use a pRS426 vector as taught by Sun and substituting the green fluorescent protein gene with the gene encoding nerolidol synthase taught by Su in order to express the nerolidol synthase. One of ordinary skill in the art would be motivated to do so, since Sun teaches a pRS426 vector with a promoter that increased protein production and this would be beneficial in the production of nerolidol synthase. One of ordinary skill in the art would have expectations of success in doing so from the combined teachings of Su and Sun who provide all the teachings, methods, and compositions needed to do so.
Therefore, claim 10 is rejected under 35 U.S.C. 103 as being unpatentable over Su et al. (Scientific Reports, Vol. 7:40851; published January 2017; PMID: 28128232 as applied to claim 9 above, and further in view of Sun et al. (Biotechnology and Bioengineering, Vol. 109, pg. 2082-2092, published August 2012).
Claim 15 is rejected under 35 U.S.C. 103 as being unpatentable over Su et al. (Scientific Reports, Vol. 7:40851; published January 2017; PMID: 28128232), hereinafter referred toa s Su, as applied to claim 12 above, and further in view of Nowroozi et al. (Biotechnology Products and Process Engineering, Vol. 98, pg. 1567-1581; published online November 21, 2013, cited in the IDS), hereinafter referred to as Nowroozi.
The teachings of Su as applied to claim 12 are summarized above.
Su does not each that the recombinant strain comprising the polynucleotide molecule comprising at least one of nucleotide sequences encoding the nerolidol synthase is configured for endogenously and/or exogenously expressing at least one of acetoacetyl coenzyme A thiolase, hydroxy-methylglutaryl-CoA synthase, hydroxy-methylglutaryl-CoA reductase, mevalonate kinase, mevalonate-5-phosphatase kinase, mevalanote pyrophosphate decarboxylase, isoprene pyrophosphate isomerase, and farnesyl pyrophosphate synthase..
However, Nowroozi teaches that the genes encoding the mevalonate-based farnesyl pyrophosphate (FPP) biosynthetic pathway, were encoded in two operons and expressed in E. coli to increase the production of sesquiterpenes (terpene). Nowroozi teaches that the pMBIS harbors genes for the mevalonate pathway from mevalonate to farnesyl pyrophosphate (FPP) (see pg 1568). The MBIS operon (mevK (mevalonate kinase), pmk, pmd (mevalonate pyrophosphate decarboxylase), idi, and ispA (farnesyl pyrophosphate synthase) was cloned into pBBR1MCS, a low copy plasmid with an IPTG inducible lac promoter to create pMBIS. Nowroozi teaches that the MBIS operons were cloned into a pTrc99a derivative to create a pTRc-M.ADS-MBIS1-9. (ADS is the amorphadiene synthase gene, a terpene synthase). Nowroozi teaches that E. coli DH1 was transformed with the plasmid and cultures were grown (see pg. 1571).
It would have been obvious to one of ordinary skill in the art of protein engineering before the effective date of the current instant application to modify the nucleic construct taught by Su to further comprise an operon containing mevalonate kinase, mevalonate pyrophosphate decarboxylase, and farnesyl pyrophosphate synthase, as taught by Nowroozi and incorporating the construct into the E. coli host cell for expression in order to increase the production of the terpene, nerolidol. One of ordinary skill in the art would be motivated to do so since, Nowroozi teaches that the MBIS operon which comprises mevalonate kinase, mevalonate pyrophosphate decarboxylase, and farnesyl pyrophosphate synthase, may be used to improve production of the product formed by the terpene synthase, ADS. As nerolidol synthase also dependent on the mevalonate-based farnesyl pyrophosphate biosynthetic pathway since the immediate precursor to nerolidol is FPP as evidenced by BenchChem Technical publication, (see pg. 2, published 2026, cited in PTO-892), one of ordinary skill in the art would be motivated to incorporate the operon into the nucleic acid construct comprising nerolidol synthase and expressing it in E. coli to achieve improved production of nerolidol. One of ordinary skill in the art would have expectations of success in doing so from the combined teachings of Su and Nowroozi.
Therefore, claim 15 is rejected under 35 U.S.C. 103 as being unpatentable over Su et al. (Scientific Reports, Vol. 7:40851; published January 2017; PMID: 28128232 as applied to claim 12 above, and further in view of Nowroozi et al. (Biotechnology Products and Process Engineering, Vol. 98, pg. 1567-1581; published online November 21, 2013, cited in the IDS).
Conclusion
No claims are allowed.
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/GEORGE THEMISTOCLIS LOUNTOS/Examiner, Art Unit 1652
/ROBERT B MONDESI/Supervisory Patent Examiner, Art Unit 1652
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