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 .
Election/Restrictions
Applicant's election with traverse of Group I (claims 21-28) in the reply filed on 12/15/2025 and the following species is acknowledged:
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The traversal is on the ground(s) that “the special technical feature of the claimed invention resides not in the routine selection of one known enzyme over another for a sub-step, but in the novel design and integration of the overall multi-enzymatic pathway to achieve de novo starch synthesis from simple precursors. This is not found persuasive because the claims do not recite a multi-enzymatic pathway such as multiple enzymes expressed in a single organism or in one reaction mixture. Rather, the claims recite separate enzymatically catalyzed step performed in a step by step manner wherein at least steps (1)-(3) of claim 12 do not require more than one enzyme to be present. Further, Wong teaches at least steps (1) and (2).
The requirement is still deemed proper and is therefore made FINAL.
Claims 15, 18, and 24-27 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected species, there being no allowable generic or linking claim. Applicant timely traversed the restriction (election) requirement in the reply filed on 12/15/2025. Claim 15 does not read on elected pathways 11 and 12, claim 18 does not read on elected pathways 17 and 18, and claims 24-27 do not read on elected methanol to formaldehyde pathway 2.
In the interest of compact prosecution, claim 29 is not withdrawn and Groups I and II are rejoined and examined herein; however, the species election requirement remains of record. In view of the withdrawal of the restriction requirement, applicant(s) are advised that if any claim presented in a divisional application is anticipated by, or includes all the limitations of, a claim that is allowable in the present application, such claim may be subject to provisional statutory and/or nonstatutory double patenting rejections over the claims of the instant application. Once the restriction requirement is withdrawn, the provisions of 35 U.S.C. 121 are no longer applicable. See In re Ziegler, 443 F.2d 1211, 1215, 170 USPQ 129, 131-32 (CCPA 1971). See also MPEP § 804.01.
Claim Objections
Claims 13-17, 19, and 20 are objected to because of the following informalities:
Claim 13 recites reaction 9 and reaction 10; clam 14 recites reaction 15; claim 15 recites reaction 13 or 15; claim 17 recites reaction 11 and reaction 12; claim 17 recites reaction 16 and reaction 20; claim 19 recites reaction 17 and reaction 18; and claim 20 recites reaction 8. “Where possible, claims are to be complete in themselves. Incorporation by reference to a specific figure or table "is permitted only in exceptional circumstances where there is no practical way to define the invention in words and where it is more concise to incorporate by reference than duplicating a drawing or table into the claim. Incorporation by reference is a necessity doctrine, not for applicant’s convenience." MPEP 2173.05(s). Reference to reaction 9, reaction 10, etc., is understood as a reference to specific information in Fig. 1 and body of the specification to incorporate specific information into the claims, which is not allowed by MPEP 2173.05(s). Further, as far as reaction 9, reaction 10, etc., is understood to be a positive limitation of the claims, the same should not be recited in parenthesis.
Appropriate correction is required.
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 12-14, 16, 17, 19-23 and 28-29 (all non-withdrawn claims) 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 claims define the following compounds as follows:
Compound D: namely dihydroxyacetone;
Compound E: namely dihydroxyacetone phosphate;
Compound F: namely D-glyceraldehdye 3-phosphate;
Compound G: namely D-fructose-1,6-bisphosphate;
Compound H: namely D-fructose-6-phosphate;
Compound I: namely D-glucose-6-phospahte; and
Compound J: namely alpha-D-glucose-1-phosphate;
Compound K: namely adenosine diphosphate-alpha-D-glucose;
Compound 1: namely amylose;
Compound 2: namely amylopecitin.
The use of “namely” raises confusion if each named compound is an example of the various compounds indicated by letter or is limited to only that compound. If compound D, for example, can only be dihydroxyacetone, then recitation of compound D is unnecessary as recitation of only dihydroxyacetone would be sufficient such that the claims can be interpreted to assert that compound D and other indicated compounds can have identities other than the specific enumerated examples. For this reason an ordinarily skilled artisan cannot understand how to avoid infringement.
Several of the claims recite wherein the enzyme used “may be enzyme combination,” may be a 6single enzyme, “may be done,” “may be the following enzyme combinations” and similarly “may be” phraseology, particularly, claims 12-14, 16, 17, 19, and 22. The phrase "may be" 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). That is, it is unclear if the various claim limitations after “may be” are positive limitations of the claims or unrequired claim features that are merely exemplary. For this reason, an ordinarily skilled artisan cannot determine how to avoid infringement.
Regarding claim 29, the phrase "preferably" renders the claim indefinite because it is unclear whether the limitation(s) following the phrase are part of the claimed invention. See MPEP § 2173.05(d). As explained above, it is unclear if the limitations following “preferably” are required or exemplary such that an ordinarily skilled artisan cannot determine how to avoid infringement.
Further in claim 29, “A Markush grouping is a closed group of alternatives, i.e., the selection is made from a group "consisting of" (rather than "comprising" or "including") the alternative members. Abbott Labs., 334 F.3d at 1280, 67 USPQ2d at 1196. If a Markush grouping requires a material selected from an open list of alternatives (e.g., selected from the group "comprising" or "consisting essentially of" the recited alternatives), the claim should generally be rejected under 35 U.S.C. 112(b) as indefinite because it is unclear what other alternatives are intended to be encompassed by the claim.” MPEP 2173.05(h). Claim 29 recites Markush groups in the form of “includes, but is not limited to” such that the recited Markush groups are an open list of alternatives and are rejected under 35 U.S.C. 112(b) as indefinite because it is unclear what other alternatives are intended to be encompassed by the claim.
Claim 28 recites the limitation "the . . . sub-steps" in line 2. There is insufficient antecedent basis for this limitation in the claim. Claim 12 from which claim 28 depends does not recite sub-steps such that it is unclear as to what claim limitation “the” sub-steps as recited in claim 28 references. A sub-step is considered to be different from any of steps (1), (2) and (3) recited in claim 12 such that is it unclear how infringement of claim 28 is avoided.
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.
Claim(s) 29 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Nguyen et al. (Reconstruction of Methanol and Formate Metabolic Pathway in Non-native Host for Biosynthesis of Chemicals and Biofuels, Biotechnol. Bioprocess Eng. 21, 2016, 477-82).
Nguyen, abstract, states: “One-carbon feedstock such as methanol and formate has attracted much attention as carbon substrate of industrial biotechnology for production of value-added chemicals and biofuels.” Nguyen, Fig. 5, is as follows:
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Claim 29 reads on synthesis of dihydroxyacetone occurring in an in vitro system (purified enzymes and substrates) and in vivo in an engineered host cell. As such, Fig. 5 discloses a method for synthesis of dihydroxyacetone (DHA) having a pathway of converting methanol into formaldehyde and formaldehyde to DHA by one or more enzymes having such activity as to anticipate claim 29.
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.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claim(s) 12-13, 17, and 28 is/are rejected under 35 U.S.C. 103 as being unpatentable over Wong et al. (Synthesis of sugars by aldolase-catalyzed condensation reaction, J. Org. Chem 48, 1983, 3199-3205) (previously cited) further in view of Ohdan et al. (Enzymatic synthesis of amylose, Biocatalysis and Biotransformation 24, 2006, 77-81) and Leaver et al. (WO 98/023757 A1).
Wong, abstract, teaches enzymatic production of glucose-6-phosphate from dihydroxyacetone by several enzymes including glycerol kinase, triose phosphate isomerase, aldolase and additional enzymes as show in Scheme III. Wong, abstract and Scheme III, describe preparation of dihydroxyacetone phosphate (DHAP) from dihydroxyacetone by action of a glycerol kinase and conversion of DHAP to D-glycerol-3-phosphate by action of triose phosphate isomerase (TPI), condensation of DHAP and D-glyerol-3-phosphate by action of aldolase to produce fructose-1,6-bisphosphate (FDP), conversion of FDP to fructose-6-phosphate by non-enzymatic means, and conversion of fructose-6-phosphate to glucose-6-phosphate (G6P) (i.e. compound “I”). The above is a description of the following by Wong:
step (1): converting the starting material compound D, namely dihydroxyacetone, into a compound F, namely D-glyceraldehyde 3-phosphate, by catalysis with one or more enzymes; and
step (2): converting the compound F obtained in step (1) into a compound I, namely D-glucose- 6-phosphate, by catalysis with one or more enzymes.
Wong, page 3205, left col. (bottom) makes clear that glucose-6-phosphate and fructose-6-phosphate as discussed by Wong are D-glucose-6-phosphate and D-fructose-6-phosphate.
However, Wong does not teach step (3) as recited in claim 12.
Wong, pages 3202-03 teaches: “Aldolase-catalyzed condensation provides a practical route to a wide variety of simple sugars and sugar derivatives, and especially to those (glucose, fructose, and derivatives) centrally important in intermediary metabolism. The procedure has the advantage that it is applicable to unprotected sugars in aqueous solution at pH 7. Epimeric mixtures can, in favorable cases, be separated without chromatography by taking advantage of substrate-selective enzymatic phosphorylation. The sugar phosphates prepared here are of 80-90% purity.” “Overall, these reactions seem to have genuine value as a method of synthesis for polyhydroxy compounds.”
That is, the teachings of Wong are directed towards the preparation of sugar phosphates (e.g. glucose-6-phosphate) that are otherwise difficult or costly to obtain for further use in applications wherein the same are required.
Ohdan teaches a further application of phosphorylated glucose. “Amylose is a linear polymer of a-1,4-linked glucose and is expected to be used in various industries as a functional biomaterial. However, pure amylose is currently not available for industrial purposes, since the separation of natural amylose from amylopectin is difficult. It is known that amylose has been synthesized using various enzymes. Glucan phosphorylase, together with its substrate, glucose-1-phosphate, is the most suitable system for the production of amylose since the molecular size of amylose can be controlled precisely. However, the problem with this system is that glucose-1-phosphate is too expensive for industrial purposes. This review summarizes our work on the enzymatic synthesis of essentially linear amylose, together with recent progress in the production of synthetic amylose using sucrose or cellobiose through the combined actions of phosphorylases.” Ohdan, abstract.
“Glucan phosphorylase (GP; EC 2.4.1.1) catalyzes the reverse reaction of the phosphorylation of α-1,4 glucan, as shown in the following equation:
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Amylose can be synthesized when glucose 1-phosphate (G-1-P) is in excess, and where a glucan synthetic reaction predominates. It has been reported that essentially linear amylose can be synthesized using potato GP, and the Mw of amylose can be controlled by the G-1-P/primer molar ratio.” Ohdan, pages 78-79. Table II of Ohdan reports production of amylose using combination of specific primers catalyzed by GP with 50 mM glucose-1-phosphate. As indicated in the preceding equation, all glucose and derivates thereof are of D-glucose.
While Ohdan reports that glucose 1-phosphate is an expensive chemical precluding its industrial use, Ohdan in Table II nevertheless reports synthesis of amylose/starch using glucose-1-phosphate as a substrate for GP. As discussed above, Wang reports production of glucose phosphate (i.e. glucose-6-phosphate) in a “practical” manner. As far as repeating the amylose production reported in Table II of Ohdan requires obtaining D-glucose-1-phosphate (G1P) from some source, an ordinarily skilled artisan at the time of filing would have been motivated to obtain such G1P from any suitable source including the “practical” sources reported by Wong. Ohdan requires G1P while Wang reports production of glucose-6-phosphate. Leaver relates to genetically modified potato plants for increased starch content. As discussed, Ohdan teaches potato GP for starch/amylose production. As shown in Fig. 1A of Leaver, it is well understood that amylose in potato and other plants is produced from glucose-6-phoshate by the activity of phosphoglucomutase converting glucose-6-phosphate to glucose-1-phosphate (D isomers)f, which then serves as a substrate for starch synthesis either directly as taught by Ohdan or by further conversion to ADP-glucose as taught by Leavers, Fig. 1A. As such, at the time of filing, an ordinarily skilled artisan at the time of filing would have been motivated to convert D-glucose-6-phosphate as produced by the methods of Wong to D-glucose-1-phosphate by applying activity of a suitable phosphoglucomutase as a further valuable glucose phosphate that can be produced from DHA/DHAP as taught by Ohdan. An ordinarily skilled artisan at the time of filing would have been motivated to do this since it is understood that glucose-6-phosphate is a precursor to starch/amylose biosynthesis as taught by Leaver but requiring further conversion/isomerization to glucose-1-phosphate that is readily performed by the activity of phosphoglucomutase. Once when glucose-1-phosphate is produced by the “practical” methods of Ohdan plus an additional step with phosphoglucomutase, an ordinarily skilled artisan at the time of filing would have been motivated to apply such produced glucose-1-phosphate to any suitable application including the methods taught in Table II of Ohdan for a amylose/starch synthesis with GP as an enzyme, which further meets the features of claim 17.
Regarding claim 13, Wong, Scheme II, shows conversion of dihydroxyacetone to dihydroxyacetone phosphate by action of glucokinase (GK). “The biochemical route to DHAP is based on the enzymatic phosphorylation of DHA by ATP with in situ cofactor regeneration.” Wong, page 3201, left col. Then, as discussed, Wong Scheme III, shows conversion of DHAP to D-glyceraldehyde-3-phosphate by action of triosephosphate isomerase (TPI).
Regarding claim 28, at least Wong teaches the conversion of DHA to glucose-6-phosphate as a “step by step” process. More specifically, Wong, page 3203-04, describe conversion of DHA to DHAP, aldolase catalyzed condensation of DHAP and glyceraldehyde , etc., as occurring step by step such that the all of the steps discussed above are proposed or suggested by the prior art to occur step by step as opposed to a simultaneously.
Claim(s) 12-13, 17, 20 and 28 is/are rejected under 35 U.S.C. 103 as being unpatentable over Wong et al. (Synthesis of sugars by aldolase-catalyzed condensation reaction, J. Org. Chem 48, 1983, 3199-3205), Ohdan et al. (Enzymatic synthesis of amylose, Biocatalysis and Biotransformation 24, 2006, 77-81) and Leaver et al. (WO 98/023757 A1) as applied to claims 12-13, 17, and 28 above, and further in view of Desmons et al. (Formaldehyde as a Promising C1 Source, ACS Catalysis 9, 2019, 9575-88).
Regarding claim 20, as discussed, dihydroxyacetone (DHA) is the starting material shown in Scheme II and III of Wong through which DHAP and glucose-6-phosphate is produced. Desmons teaches that DHAP can be advantageously produced from formaldehyde. “In the context of the depletion of fossil resources, formaldehyde is an emerging C1 source exhibiting high and versatile reactivity.” Desmons, abstract. Figure 1 of Desmons shows the following reaction wherein the compound of the right is DHA:
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As such, since Desmons teaches that reaction of formaldehyde with a single enzyme being formolase to produce DHA is a desirable means of producing DHA, an ordinarily skilled artisan would have been motivated to provide DHA by any suitable means in order to practice the methods of Wong including a step of converting formaldehyde into DHA with a formolase enzyme having activity for the same.
Claim(s) 12-13, 17, 20-23 and 28-29 is/are rejected under 35 U.S.C. 103 as being unpatentable over Wong et al. (Synthesis of sugars by aldolase-catalyzed condensation reaction, J. Org. Chem 48, 1983, 3199-3205), Ohdan et al. (Enzymatic synthesis of amylose, Biocatalysis and Biotransformation 24, 2006, 77-81), Leaver et al. (WO 98/023757 A1) and Desmons et al. (Formaldehyde as a Promising C1 Source, ACS Catalysis 9, 2019, 9575-88) as applied to claims 12-13, 17, 20 and 28 above, and further in view of Chistoserdova, Applications of methylotrophs, Curr. Opinion Biotechnol. 50, 2018, 189-94).
Regarding claims 21-23 and 29, Desmons, page 9575, left col., teaches: “For the chemical industry, formaldehyde is an important building block, and more than 20 million tons of it are produced each year, mostly from partial oxidation of methanol.” As such, it is understood that that formaldehyde is produced from methanol. Chistoserdova, page 192, teaches the following:
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As discussed, it is known in the prior art to employ formolase to convert formaldehyde to DHA. The claims are directed include in vitro reactions not taking place in a host cell. Regardless, Chistoserdova teaches that it is known to provide for the formaldehyde substrate to be utilized by formolase by oxidation of methanol with a Mdh (methanol dehydrogenase) enzyme that converts methanol to formaldehyde. As such, in any system employing a formolase enzyme, whether in vitro or within a host cell, it is predictable and suggested by the prior art for the needed formaldehyde substrate to be provided by an enzymatically catalyzed conversion of methanol to formaldehyde, which further meets the enzyme combination II-1-d and III-2-d recited in claims 22 and 23 with the remaining enzymes recited in such combination discussed above.
Claim(s) 12-14, 16-17 and 28 is/are rejected under 35 U.S.C. 103 as being unpatentable over Wong et al. (Synthesis of sugars by aldolase-catalyzed condensation reaction, J. Org. Chem 48, 1983, 3199-3205), Ohdan et al. (Enzymatic synthesis of amylose, Biocatalysis and Biotransformation 24, 2006, 77-81) and Leaver et al. (WO 98/023757 A1) as applied to claims 12-13, 17, and 28 above, and further in view of Fujita et al. (Purification and Properties of Fructose-1,6-bisphosphatase of Bacillus subtilis, J. Biol. Chem. 254, 1979, 5340-49).
Regarding claims 14 and 16, as discussed, Wong Scheme III, shows enzymatic conversion of glyceraldehyde-3-phosphate (G3P) to D-fructose-1,6-bisphosphate catalyzed by aldolase, a singe enzyme having function of catalyzing conversion of G3P to D-F6P. However, further conversion of D-fructose-1,6-bisphosphate is shown in Scheme III of Wong to be a non-enzymatic acid hydrolysis to fructose-6-phosphate.
However, conversion of D-fructose-1,6-bisphosphate to D-fructose-6-phosphate is further known to be catalyzed enzymatically by fructose-1,6-bisphosphatase as explained by abstract of Fujita. Considering that all of the other steps illustrated in Scheme III of Wong are catalyzed by enzymes, an ordinarily skilled artisan at time of filing would have been motivated to substitute an enzyme, D-fructose-1,6-bisphosphate, in replacement for a non-enzymatic dephosphorylation of fructose-1,6-bisphosphatase with an expectation of success in producing the same product being fructose-6-phosphate.
As discussed, Wong teaches that any produced fructose-6-phosphate is converted into D-glucose-6-phosphate by a single phosphoglucoisomerase enzyme.
Claim(s) 12-13, 17, 19 and 28 is/are rejected under 35 U.S.C. 103 as being unpatentable over Wong et al. (Synthesis of sugars by aldolase-catalyzed condensation reaction, J. Org. Chem 48, 1983, 3199-3205), Ohdan et al. (Enzymatic synthesis of amylose, Biocatalysis and Biotransformation 24, 2006, 77-81) and Leaver et al. (WO 98/023757 A1) as applied to claims 12-13, 17 and 28 above, and further in view of Fu et al. (Mutagenesis of the glucose-1-phosphate-binding site of Potato Tuber ADP-glucose pyrophosphorylase, Plant Physiol. 17, 1998, 989-996).
Regarding claim 19, in addition to direct incorporation of glucose-1-phosphate into amylose by enzymatic activity of GP as discussed in Table II of Ohdan, Ohdan, page 78, left col., further teaches the following:
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ADP-glucose (ADPG) is understood to be adenosine diphosphate-alpha-D-glucose in view of the produced 1,4-alpha-D-glucoysl product produced, wherein the starch synthase reaction is also shown in Fig. 1A of Ohdan. While Ohdan states that ADPG is not available on an industrial scale, production of ADPG is taught by the prior art. For example, Fu, abstract, teach that ADP-glucose pyrophosphorylase can be applied in in vitro to convert glucose-1-phosphate into ADPG wherein “ATP, ADPGlc, Glc-1-P, Man-1-P, Gal-1-P, GlcUA-1-P, 3PGA, and PPi were purchased from Sigma.” Fu, page 990, left col.
Fine chemicals that are purchased from a commercial supplied are ultimately produced by some means. Again, Wong teaches “Overall, these reactions seem to have genuine value as a method of synthesis for polyhydroxy compounds” specifically including activated glucose compounds including glucose-6-phosphate that is readily convertible to glucose-1-phosphate by enzymatic reaction. Fu teaches that glucose-1-phosphate can be in turn readily converted to ADPG by in vitro enzymatic reaction as shown in Table 1 of Fu. As far as Ohdan directly teaches that starch synthase enzyme can be employed in vitro to produce amylose utilizing a ADPG substrate, an ordinarily skilled artisan at time of filing would have been motivated to provide ADPG as a substrate for the same by any appropriate means suggested in the art that includes production of glucose-6-phosphate as taught by Wong, production of glucose-1-phosphate by application of phosphoglucomutase as taught by Leaver, and then production of ADPG by activity of ADP-glucose pyrophosphorylase as taught by Fu.
Conclusion
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/TODD M EPSTEIN/Primary Examiner, Art Unit 1652