Patent Application 18032129 - ENGINEERING INCREASED SUBERIN LEVELS BY ALTERING

Title: ENGINEERING INCREASED SUBERIN LEVELS BY ALTERING GENE EXPRESSION PATTERNS IN A CELL-TYPE SPECIFIC MANNER

Application Information

Invention Title: ENGINEERING INCREASED SUBERIN LEVELS BY ALTERING GENE EXPRESSION PATTERNS IN A CELL-TYPE SPECIFIC MANNER
Application Number: 18032129
Submission Date: 2025-05-16T00:00:00.000Z
Effective Filing Date: 2023-04-14T00:00:00.000Z
Filing Date: 2023-04-14T00:00:00.000Z
National Class: 800
National Sub-Class: 278000
Examiner Employee Number: 99567
Art Unit: 1663
Tech Center: 1600

Rejection Summary

102 Rejections: 2
103 Rejections: 2

Cited Patents

The following patents were cited in the rejection:

US 0002455🔗

Office Action Text

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 .
Restrictions/Elections
1. The Office acknowledges receipt of Applicant’s restriction election filed March 18, 2025. Applicant elects Group I, claims 1-6 and 22, drawn to a nucleic acid molecule comprising a nucleic acid sequence encoding SEQ ID NO:14. Applicant further elects the species of SEQ ID NO:2, the HORST gene promoter. Because applicant did not distinctly and specifically point out any supposed errors in the species election requirement, the election has been treated as an election without traverse (MPEP § 818.01(a)).
The requirement is deemed proper and is made FINAL.
Claim Status
2. Claims 1-6 and 22 are pending and under examination to the extent of the elected species of SEQ ID NO:2, the HORST gene promoter.
Claims 7-11 and 13-20 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. The election made in the reply filed on March 13, 2025 has been treated as an election without traverse (MPEP § 818.01(a)).
Claims 12, 21, and 23-27 are cancelled.
Priority
3. This application is a 371 of International Application No. PCT/US2021/055246 filed on September 15, 2021. The Office acknowledges receipt of Applicant’s domestic priority document Provisional Application No. 63/093,205 filed on September 17, 2020.
Information Disclosure Statement
4. The information disclosure statements (IDS) submitted on July 28, 2023, November 14, 2024, and January 08, 2025 are in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statements are being considered.
Specification
5. The disclosure is objected to because of the following:
The abstract of the disclosure does not commence on a separate sheet in accordance with 37 CFR 1.52(b)(4) and 1.72(b). A new abstract of the disclosure is required and must be presented on a separate sheet, apart from any other text.
Appropriate correction is required.
Claim Objections
6. Claims 1-6 and 22 are objected to because of the following:
Claim 1, ln. 3 contains a typographical error; “a nucleic acid set forth” should be amended to “a nucleic acid sequence set forth.”
Claim 22 contains typographical errors; the word “the” should be inserted before “FACT”, “HORST”, “ASFT”, “GPAT5”, “RAPLH”, and “MYB84” for grammatical correctness. Additionally, standard scientific notation requires that the names of genes be italicized. Accordingly, “FACT”, “HORST”, “ASFT”, “GPAT5”, “RAPLH”, and “MYB84” should each be italicized within claim 22.
Dependent claims are included.
Appropriate correction is required.
Claim Rejections - 35 USC § 112(b)
7. 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.
8. Claims 1-6 and 22 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.
The metes and bounds of claim 1 are indefinite because an amino acid sequence cannot comprise any degree of sequence identity/homology to a nucleic acid. Thus, it is unclear what is encompassed by the recitation of a MYB41 amino acid sequence with at least 80% sequence homology to a nucleic acid set forth in SEQ ID NO:13 or SEQ ID NO:15.
The metes and bounds of claim 1 are indefinite because it is unclear what sequences are encompassed by the recitation of sequences having a certain degree of “homology” to SEQ ID NO:14. In [00102], Applicant states that the term “homology” is known in the art and refers to sequences sharing a common ancestor/family member and are determined based on the degree of sequence identity. Applicant further discloses the terms “homology”, “homologous”, “substantially similar”, and “corresponding substantially” to be interchangeable [00102]. Accordingly, it is unclear what degree of sequence/structural identity is shared between SEQ ID NO:14 and a sequence having 80% sequence homology to SEQ ID NO:14. If Applicant intends to recite sequences having 80% sequence identity to SEQ ID NO:14, it is recommended Applicant amended all recitations of “homology” to “identity” within the claims. See also: claims 3-4.
Dependent claims are included.
Appropriate correction is required.
Claim Rejections - 35 USC § 102
9. 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.

10. Claims 1, 3-4, and 6 are rejected under 35 U.S.C. 102(a)(2) as being anticipated by Epple et al. (US-2023/0002455-A1, published 01/05/2023 (A)).
Epple discloses the Arabidopsis plants comprising increased production and/or accumulation of a Myb41-type transcription factor (Abstract), the role of Myb41 in several stress responses [0021], and increased/ectopic suberin content in plants overexpressing Myb41 [0022].
Regarding claims 1 and 4, the Office notes that the overexpression of a Myb41 protein, as recited by Epple ([0035], [0043], [0124]), requires the sequence encoding said protein be operably linked to a heterologous promoter. The Office also notes that the phenotype resulting from the expression of a nucleic acid sequence results from the activity of the protein encoded therein. Furthermore, the activity of a protein is inherent to the structure/sequence of said protein. Therefore, the Myb41 protein taught by Epple, which is identical to SEQ ID NO:14, inherently has the same activity as SEQ ID NO:14. Accordingly, Epple teaches an isolated nucleic acid molecule comprising a nucleic acid sequence encoding a MYB41 amino acid sequence (SEQ ID NO:2) having 100% sequence identity to instant SEQ ID NO:14, wherein said nucleic acid molecule is operably linked to a nucleic acid sequence encoding a heterologous promoter, wherein expression of the nucleic acid molecule in a plant results in increased levels of suberin as compared to wild-type check plants lacking the nucleic acid molecule (Abstract; claim 1; [0022], [0024-0029], [0031], [0040]). Thus, Epple teaches each limitation of claim 1 and claim 4.
Regarding claim 3, in addition to the teachings discussed above, the Myb41 amino acid sequence taught by Epple has at least 99% sequence identity to SEQ ID NO:14.
Regarding claim 6, in addition to the teachings discussed above, Epple teaches a transformation vector comprising the nucleic acid molecule(s) of claim 1 (Fig. 2; [0026]; [0040]).
Accordingly, the claimed invention is anticipated by the prior art.
11. Claims 1, 3-4, and 6 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Kosma et al. (The Plant Journal. 2014; 80:216-229 (Applicant’s IDS)), hereinafter “Kosma 2014”, as evidenced by GenBank Accession No. NP_194540 (GenBank. 2019 (Applicant’s IDS)).
Kosma 2014 discloses the role of the Arabidopsis transcription factor MYB41 (AtMYB41/At4g28110) in suberin synthesis and deposition in both A. thaliana and Nicotiana benthamiana (Abstract; p. 222, Table 1). GenBank Accession No. NP_194540 discloses that AtMYB4/At4g28110 comprises an amino acid sequence that is identical to SEQ ID NO:14. Accordingly, the AtMYB41 protein disclosed by Kosma 2014 is identical to the instant SEQ ID NO:14.
Regarding claim 1, Kosma 2014 teaches an isolated nucleic acid molecule comprising a nucleic acid sequence encoding a MYB41 amino acid sequence having 100% sequence identity to SEQ ID NO:14 (Abstract; p. 226, right column, “Plasmid construction for transient overexpression”), wherein said nucleic acid molecule is operably linked to a nucleic acid sequence encoding a heterologous promoter (p. 226, right column, “Plasmid construction for transient overexpression”), wherein expression of the nucleic acid molecule in a plant results in increased levels of suberin as compared to wild-type check plants lacking the nucleic acid molecule (Abstract; p. 226, left column, “Biological function of AtMYB41”).
Regarding claim 3, in addition to the teachings discussed above, the MYB41 amino acid sequence taught by Kosma 2014 has at least 99% sequence identity to SEQ ID NO:14, as evidenced by GenBank Accession No. NP_194540.
Regarding claim 4, in addition to the teachings discussed above, Kosma 2014 teaches a MYB41 amino acid sequence having 100% sequence identity to SEQ ID NO:14.
Regarding claim 6, in addition to the teachings discussed above, Kosma 2014 teaches a transformation vector comprising the nucleic acid molecule(s) of claim 1 (p. 226, right column, “Plasmid construction for transient overexpression”).
Accordingly, the claimed invention is anticipated by the prior art.
Claim Rejections - 35 USC § 103
12. 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.
13. Claims 2 and 22 are rejected under 35 U.S.C. 103 as being unpatentable over Kosma et al. (The Plant Journal. 2014; 80:216-229 (Applicant’s IDS)), hereinafter “Kosma 2014”, as evidenced by GenBank Accession No. NP_194540 (GenBank. 2019 (Applicant’s IDS)), in view of Kosma et al. (Plant Physiology. 2012; 160:237-248 (Applicant’s IDS)), hereinafter “Kosma 2012”.
The teachings of Kosma 2014 are as discussed above in the rejections of claims 1, 3-6 and 22 under 35 U.S.C. 102(a)(1).
Regarding claims 2 and 22, in addition to the teachings discussed above, Kosma 2014 teaches increased levels of suberin in existing cells (p. 220, left column, “Overexpression of AtMYB41 increases the abundance of suberin but not cuticle biosynthetic gene transcripts”; p. 220, Fig. 3; p. 222, Table 1; p. 225, right column, first full paragraph).
Kosma 2014 is silent to the levels of suberin in periderm cells and to the production of new periderm cells.
Kosma 2012 teaches the FACT gene, the activity of its promoter in suberized tissues, including peridermal tissues (p. 238, right column, final paragraph), and suggests the FACT gene locus is involved in suberin-related processes (Abstract; p. 239, left column, first full paragraph).
The combination of Kosma 2014 and Kosma 2012 teaches an isolated nucleic acid molecule comprising a nucleic acid sequence encoding a MYB41 amino acid sequence having 100% sequence identity to SEQ ID NO:14, wherein said nucleic acid molecule is operably linked to a nucleic acid sequence encoding a heterologous FACT gene promoter, wherein expression of the nucleic acid molecule in a plant results in increased levels of suberin as compared to wild-type check plants lacking the nucleic acid molecule and wherein the increased levels of suberin occur by generating additional periderm cells or depositing more suberin in existing periderm cells.
The level of ordinary skill in the plant biotechnology art is high as evidenced by Kosma 2014 and Kosma 2012. It would have been prima facie obvious for one of ordinary skill in the art to express the recited MYB41 amino acid sequence under the control of the FACT gene promoter because Kosma 2014 teaches the role of MYB41 in increasing suberin content and Kosma 2012 teaches the role of the FACT gene promoter in directing gene expression to suberized tissues, such as the periderm (Kosma 2012; p. 238, right column, final paragraph). One of ordinary skill in the art would be motivated to express the recited MYB41 amino acid sequence under the control of the FACT gene promoter because Kosma 2014 teaches that ectopic expression of MYB41 causes developmental defects (p. 217, right column, first and second paragraphs); thus, one of ordinary skill would be motivated to restrict expression of the protein to the tissues in which suberin natively accumulates to minimize the impacts of ectopic suberin synthesis (i.e, the FACT gene promoter). Finally, one of ordinary skill in the art would be motivated to produce a plant comprising increased suberin content because of suberin’s role in various structural development and environmental/stress responses (Kosma 2014; Abstract; p. 216, left column, first paragraph). Accordingly, one of ordinary skill in the art would have been motivated to produce the claimed invention without any surprising or unexpected results.
14. Claims 2, 5, and 22 are rejected under 35 U.S.C. 103 as being unpatentable over Kosma et al. (The Plant Journal. 2014; 80:216-229 (Applicant’s IDS)), hereinafter “Kosma 2014”, as evidenced by GenBank Accession No. NP_194540 (NCBI. 2019 (Applicant’s IDS)), in view of Hofer et al. (Journal of Experimental Botany. 2008; 59(9):2347–2360 (U)), further in view of GenBank Accession No. AB016885 (NCBI. 2004 (V)), as evidenced by NCBI Reference Sequence: NM_125276.2 (NCBI. 2014 (W)).
Regarding claims 2, 5, and 22, the teachings of Kosma 2014, as evidenced by GenBank Accession No. NP_194540, are as discussed above.
Kosma 2014 does not teach a HORST promoter (claim 22) or a promoter comprising SEQ ID NO:2 (claim 5), which Applicant discloses as the nucleic acid sequence of the HORST gene promoter (Applicant’s disclosure; [00168]; p. 47, Table 2).
Hofer teaches that the cytochrome p450 gene CYP86A1, which is also annotated as the HORST gene (p. 2352, “horst knock-out mutants have a highly modified and reduced root suberin”), is a key enzyme for suberin biosynthesis (Abstract).
GenBank Accession No. AB005234.1 teaches A. thaliana genomic DNA, chromosome 5, TAC clone:K19M22 which comprises an isolated nucleic acid sequence comprising a cytochrome P450 gene and promoter sequence wherein said cytochrome P450 gene is identical to the CYP86A gene sequence as evidenced by NCBI Reference Sequence: NM_125276.2 and wherein said promoter sequence is identical to SEQ ID NO:2 (see Reference V, pp. 27-28, which displays an alignment of SEQ ID NO:2 with the sequence taught by GenBank Accession No. AB005234.1).
Regarding claims 2, 5, and 22, the combination of Kosma 2014, Hofer, and GenBank Accession No. AB005234.1 teaches an isolated nucleic acid molecule comprising a nucleic acid sequence encoding a MYB41 amino acid sequence having 100% sequence identity to SEQ ID NO:14, wherein said nucleic acid molecule is operably linked to a nucleic acid sequence encoding a heterologous FACT gene promoter, wherein expression of the nucleic acid molecule in a plant results in increased levels of suberin as compared to wild-type check plants, wherein the heterologous promoter comprises the HORST promoter having the nucleic acid sequence of SEQ ID NO:2.
The level of ordinary skill in the plant biotechnology art is high as evidenced by Kosma 2014 and Hofer. It would have been prima facie obvious for one of ordinary skill in the art to express the recited MYB41 amino acid sequence under the control of the HORST gene promoter (of SEQ ID NO:2) because Kosma 2014 teaches the role of MYB41 in increasing suberin content and Hofer teaches the role of CYP86A/HORST in promoting suberin biosynthesis. One of ordinary skill in the art would be motivated to express the recited MYB41 amino acid sequence under the control of the HORST gene promoter, SEQ ID NO:2, because Kosma 2014 teaches that ectopic expression of MYB41 causes developmental defects (p. 217, right column, first and second paragraphs); thus, one of ordinary skill would be motivated to restrict expression of the protein to the tissues in which suberin natively accumulates to minimize the impacts of ectopic suberin synthesis. Therefore, one of ordinary skill in the art would be motivated to express MYB41 under the control of a promoter known in the art to regulate the expression of genes that control suberin biosynthesis (i.e., the CYP86A/HORST promoter of SEQ ID NO:2). Finally, one of ordinary skill in the art would be motivated to produce a plant comprising increased suberin content because of suberin’s role in structural development and environmental/stress responses (Kosma 2014; Abstract; p. 216, left column, first paragraph). Accordingly, one of ordinary skill in the art would have been motivated to produce the claimed invention without any surprising or unexpected results.
Conclusion
15. No claim is allowed.
Examiner’s Contact Information
16. Any inquiry concerning this communication or earlier communications from the examiner should be directed to DEQUANTARIUS JAVON SPEED whose telephone number is (703)756-4779. The examiner can normally be reached M-F; 9AM-5PM ET.
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/DEQUANTARIUS JAVON SPEED/Junior Examiner, Art Unit 1663
/Amjad Abraham/SPE, Art Unit 1663