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 .
DETAILED ACTION
Claims 1-16 are pending and under examination.
Claim Objections
Claims 6, 8, 9-11, and 14 are objected to because they . The following amendment is suggested:
Claim 6. A composition comprising (i) the polypeptide of claim 1, (ii) a compound comprising a reactive group, and (iii) a nucleotide sugar.
Claim 8. The composition according to claim 6, wherein the nucleotide sugar is UDP-glucose.
Claim 9. A kit comprising (i) the polypeptide of claim 1, and (ii) a polypeptide having beta-glucosidase activity.
Claim 10. A method for glycosylating a compound, comprising:
mixing (i) a compound having a reactive group, (ii) the polypeptide of claim 1, and (iii) a nucleotide sugar to form a reaction mixture; and,
obtaining a glycosylated compound from the reaction mixture.
Claim 11. The method according to claim 10, wherein the compound of (a) is an indoxyl compound, wherein the glycosylated compound obtained in (b) is a soluble glycosylated indoxyl dye-precursor, and wherein the method is performed in less than 2% free oxygen.
Claim 14. A method for dying a product, comprising:
mixing, at less than 2% free oxygen, (i) an indoxyl compound, (ii) the polypeptide of any one of claims 1-5, (iii) a nucleotide sugar, and (iv) a polypeptide having beta-glucosidase enzyme activity, to form a first reaction mixture;
obtaining a soluble glycosylated indoxyl dye-precursor from the first reaction mixture;
mixing said dye precursor, said product, and a beta-glucosidase under conditions wherein free oxygen is present to obtain a second reaction mixture; and
obtaining a dyed product from the second reaction mixture;
wherein the product is selected from the group consisting of yarn, textiles, and fabrics.
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 1-16 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.
Claim 1 recites a polypeptide having glycosyltransferase activity (enzyme classification EC:2.4.1.-). It is unclear if the enzyme having glycosyltransferase activity is required to be EC 2.4.1 as recited in parentheses, or if the enzymes in said class are merely exemplary glycosyltransferases, and thus not required.
Claims 2-16 are also rejected as they depend from claim 1.
Regarding claims 7, 11, and 14, the phrase "preferably" renders the claim indefinite because it is unclear whether the limitations following the phrase are part of the claimed invention. See MPEP § 2173.05(d).
Claim 9 recites a polypeptide having beta-glucosidase enzyme activity (enzyme classification EC 3.2.1.21). It is unclear if the claim requires that the enzyme having beta-glucosidase activity must be in enzyme class in parentheses, or if the enzymes in said class are merely exemplary beta-glucosidases.
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. The claim recites inherent characteristics of the polypeptide of claim 1, but does not recite any additional structural characteristics that further limit said polypeptide. Therefore, the claim fails to further limit the claim from which it depends.
Applicant may cancel the claim, amend the claim to place the claim in proper dependent form, rewrite the claim in independent form, or present a sufficient showing that the dependent claim complies with the statutory requirements.
Claim Rejections - 35 USC § 101 and 35 USC § 112(b)
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.
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.
MPEP § 2173.05(q) “Use” Claims, states:
Attempts to claim a process without setting forth any steps involved in the process generally raises an issue of indefiniteness under 35 U.S.C. 112(b) or pre-AIA 35 U.S.C. 112, second paragraph...
"Use" claims that do not purport to claim a process, machine, manufacture, or composition of matter fail to comply with 35 U.S.C. 101. In re Moreton, 288 F.2d 708, 709, 129 USPQ 227, 228 (CCPA 1961) ("one cannot claim a new use per se, because it is not among the categories of patentable inventions specified in 35 U.S.C. § 101 "). In Ex parte Dunki, 153 USPQ 678 (Bd. App. 1967), the Board held the following claim to be an improper definition of a process: "The use of a high carbon austenitic iron alloy having a proportion of free carbon as a vehicle brake part subject to stress by sliding friction." In Clinical Products Ltd. v. Brenner, 255 F. Supp. 131, 149 USPQ 475 (D.D.C. 1966), the district court held the following claim was definite, but that it was not a proper process claim under 35 U.S.C. 101: "The use of a sustained release therapeutic agent in the body of ephedrine absorbed upon polystyrene sulfonic acid."
Although a claim should be interpreted in light of the specification disclosure, it is generally considered improper to read limitations contained in the specification into the claims. See In re Prater, 415 F.2d 1393, 162 USPQ 541 (CCPA 1969) and In re Winkhaus, 527 F.2d 637, 188 USPQ 129 (CCPA 1975), which discuss the premise that one cannot rely on the specification to impart limitations to the claim that are not recited in the claim.
It is appropriate to reject a claim that recites a use but fails to recite steps under 35 U.S.C. 101 and 35 U.S.C. 112(b) if the facts support both rejections.
Claims 15 and 16 are rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter. The claims do not fall within at least one of the four categories of patent eligible subject matter because the claims are “use” claims that do not purport to claim a process, machine, manufacture, or composition of matter. As noted above, MPEP § 2173.05(q) states that "use" claims that do not purport to claim a process, machine, manufacture, or composition of matter fail to comply with 35 U.S.C. 101.
Claims 15 and 16 are also 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. Claims 15 and 16 are indefinite because they are “use” claims that attempt to claim a process without setting forth any steps involved in the process. As noted above, MPEP § 2173.05(q) states that attempts to claim a process without setting forth any steps involved in the process generally raises an issue of indefiniteness under 35 U.S.C. 112(b) or pre-AIA 35 U.S.C. 112, second paragraph.
Claim Rejections - 35 USC § 112(a)
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1-16 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventors, at the time the application was filed, had possession of the claimed invention.
Claims 1, 2, and 6-16 encompass a polypeptide having glycosyltransferase activity wherein the amino acid sequence has at least 75% sequence identity to SEQ ID NO:2 and comprises one or more amino acid substitutions selected from E75P, Q86K, S110V, I188L, G222D, G296L, V297G, F381V, T388A, S413K and G430K with respect to SEQ ID NO. 2, and/or (ii) amino acid residue substitutions T388C and A399C with respect to SEQ ID NO. 2. Claim 3 requires that the polypeptide of claim 1 comprises amino acid residue substitutions E75P, Q86K, S110V, I188L, G222D, G296L, V297G, S413K, and G430K with respect to SEQ ID NO. 2. Claim 4 requires that the polypeptide of claim 3 further comprises (i) one or more amino acid residue substitutions selected from F381V and T388A with respect to SEQ ID NO 2, and/or (ii) amino acid residue substitutions T388C and A399C with respect to SEQ ID NO. 2. Claim 5 requires that the polypeptide of claim 3 further comprises (i) amino acid residue substitution T388A with respect to SEQ ID NO. 2, (ii) amino acid residue substitutions F381V and T388A with respect to SEQ ID NO. 2, or (iii) amino acid residue substitutions F381V, T388C, and A399C with respect to SEQ ID NO. 2.
MPEP 2163.05 II states “the written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species. A ‘representative number of species’ means that the species which are adequately described are representative of the entire genus. Thus, when there is substantial variation within the genus, one must describe a sufficient variety of species to reflect the variation within the genus. See AbbVie Deutschland GmbH & Co., KG v. Janssen Biotech, Inc., 759 F.3d 1285, 1300, 111 USPQ2d 1780, 1790 (Fed. Cir. 2014) (Claims directed to a functionally defined genus of antibodies were not supported by a disclosure that ‘only describe[d] one type of structurally similar antibodies’ that ‘are not representative of the full variety or scope of the genus.’). The disclosure of only one species encompassed within a genus adequately describes a claim directed to that genus only if the disclosure "indicates that the patentee has invented species sufficient to constitute the gen[us].’”
The instant specification reduces to practice 12 enzyme mutants (Table 4) with either one or two substitution mutations. The specification does not disclose the entire genus of glycosyltransferase variants with up to 25% sequence divergence from instant SEQ ID NO:2. The specification dos not disclose what structural properties are required for the enzyme to maintain glycosyltransferase activity, or disclose which regions of SEQ ID NO:2 are the active site residue(s) for conserving the claimed enzyme activity. The instant specification does not disclose what structural properties are required for the enzyme to have an increased activity half-life at 45˚C compared to SEQ ID NO:2, as required by claim 2. Therefore, the disclosed species are not representative of the entire genus of claimed enzyme variants.
Dueber et al., (WO 2016/14120 A1) teaches a method for producing indigoid dye precursors using glycosyltransferase polypeptides to produce indigoid dye precursors from indole feed compounds (Abstract; paras. [0007]-[0009]). Dueber teaches a sequence (SEQ ID NO:4) with 99.2% sequence identity to instant SEQ ID NO:2. Dueber does not disclose what enzyme active site residues are responsible for glycosyltransferase activity, and does not disclose polypeptides with up to 25% sequence divergence from instant SEQ ID NO:2 that maintain glycosyltransferase activity.
In summary, neither the instant specification, nor the prior art, discloses a structure-function relationship between conserved amino acid residues in the claimed enzyme structure and the claimed enzyme activity. One of ordinary skill in the art cannot reasonably predict which 25% of SEQ ID NO:2 may be modified to generate a functional glycosyltransferase. Based on the instant disclosure, those skilled in the art would not conclude that the applicant was in possession of all claimed variants.
Pertinent Prior Art
The closest prior art reference is that of Dueber et al., (WO 2016/14120 A1; cited in the IDS filed 11/13/2024). Dueber teaches a P. tinctorium glucosyltransferase sequence (SEQ ID NO:4) that shares 99.1% sequence identity with instant SEQ ID NO:2 (see alignment below).
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Dueber teaches a method of producing an indigoid dye precursor from indole feed compounds comprising culturing a host cell that expresses the glycosyltransferase variant of SEQ ID NO:4 (paras. [0007]-[0009]). The sequence of Dueber does not comprise any of the substitution mutations recited in the instant claims.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to RACHEL EMILY MARTIN whose telephone number is (703)756-1416. The examiner can normally be reached M-Th 8:30-16:00, F 8:30-10:00 EST.
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/LOUISE W HUMPHREY/Supervisory Patent Examiner, Art Unit 1657
/RACHEL EMILY MARTIN/Examiner, Art Unit 1657
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