DETAILED ACTION
Status of the Application
Claims 1, 25, 54-65, 67, 108, 113, 119-120, 161 are pending.
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Applicant’s election with traverse of Group III, claims 1, 25, 54-65, 67, 161, drawn in part to a genetically modified cell capable of producing 6-aminocaproic acid (6ACA), the election of a genetic modification that decreases the activity of an oxidoreductase acting on an aldehyde or oxo moiety (A1), the election of spermidine and octanol as a single combination of byproducts from Table 10 or Table 11, the election of PA6 as the single combination of polymers, and the 6ACA production pathway from Figure 1 (steps A, B, C, D, N, O, P), as submitted in a communication filed on 7/28/2025 is acknowledged.
Applicant’s traverse is on the ground that in view of the substantial commonality of the subject matter of all the claims, the search for the subject matter of one of these groups will necessitate a search of the subject matter of the other group. Applicant states that no substantial burden is therefore seen in consideration of these groups in a single application. Applicant is of the opinion that examination of the non-elected claims with the elected group provides efficiency in early determination of the full scope of patent protection to be afforded in this technology. Applicant’s arguments have been fully considered but not deemed persuasive to withdraw the restriction requirement. Contrary to Applicant’s assertions, there is no substantial commonality of the subject matter of the claims, and the search for the subject matter of one of the groups will not necessitate a search of the subject matter of the other groups. The claims encompass a wide array of diverse inventions that include compositions each comprising different and unrelated compounds, and genetically engineered cells each producing different and unrelated compounds, wherein each of these engineered cells have unrelated genetic modifications which are not necessarily overlapping. It would be erroneous to assume that literature that describes (i) a composition comprising a compound would necessarily disclose a genetically engineered cell that produces said compound, (ii) a genetically engineered cell that produces one compound would necessarily disclose another genetically engineered cell that produces a different compound, (iii) a composition that comprises a compound would necessarily disclose other compositions comprising different compounds, and (iv) a genetically engineered cell that has a set of genetic modifications and produces a compound would necessarily disclosed another genetically engineered cell that produces the same compound but has a different set of genetic modifications. A comprehensive search of all the inventions would require not only different class/subclass searches which are not necessarily co-extensive but also different keyword searches in the patent and non-patent literature which are not overlapping. Thus, an examination of all the claimed inventions would impose an undue burden on the Office. The requirement is deemed proper and therefore is made FINAL.
Claims 108, 113, 119-120 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. Applicant timely traversed the restriction (election) requirement in the reply filed on 7/28/2025.
Claims 1, 25, 54-65, 67, 161 are at issue and will be examined to the extent they encompass the elected invention.
Specification
The first paragraph of the specification is objected to because it does not provide the current status of related applications (e.g., now abandoned). Appropriate correction is required.
The title of the invention is not descriptive. The title refers to a method. However, there are no method claims. A new title is required that is clearly indicative of the invention to which the claims are directed.
Priority
Acknowledgment is made of a claim for domestic priority under 35 U.S.C. 119(e) to provisional application No. 62/183,620 filed on 06/23/2015.
Acknowledgment is made of a claim for domestic priority under 35 U.S.C. 120 or 121 to US application No. 15/579,118 filed on 03/15/2018.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 9/6/2023 is acknowledged. The submissions are in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statements are being considered by the examiner.
Drawings
The drawings submitted on 9/6/2023 have been reviewed and are accepted by the Examiner for examination purposes.
Claim Objections
Claim 54 is objected to due to the recitation of “yield of target product”. The term should be amended to recite “the yield of the target product”. Appropriate correction is required.
Claim 55 is objected to due to the recitation of “yield of target product”. The term should be amended to recite “the yield of said target product”. Appropriate correction is required.
Claim 57 is objected to due to the recitation of “polymerization of target product”. The term should be amended to recite “polymerization of the target product”. Appropriate correction is required.
Claim 59 is objected to due to the recitation of “selected from PA6, … or PA6T”. The term “or” should be amended to recite “and”. Appropriate correction is required.
Claim 60 is objected to under 37 CFR 1.75 as being a substantial duplicate of claim 57. When two claims in an application are duplicates or else are so close in content that they both cover the same thing, despite a slight difference in wording, it is proper after allowing one claim to object to the other as being a substantial duplicate of the allowed claim. Since the target product of claim 57 is selected from HMD, ADA, 6ACA, CPO, CPL, LVA, and HDO in view of the definition in claim 1, the scope of claim 60 is a substantial duplicate of claim 57. See MPEP § 706.03(k).
Claim Rejections – Improper Markush Grouping
Claims 1, 25, 59-65, 161 and dependent claims 54-58, 67 are rejected on the basis that they contain an improper Markush grouping of alternatives. See In re Harnisch, 631 F.2d 716, 721-22 (CCPA 1980) and Ex parte Hozumi, 3 USPQ2d 1059, 1060 (Bd. Pat. App. & Int. 1984). A Markush grouping is proper if the alternatives defined by the Markush group (i.e., alternatives from which a selection is to be made in the context of a combination or process, or alternative chemical compounds as a whole) share a "single structural similarity" and a common use. A Markush grouping meets these requirements in two situations. First, a Markush grouping is proper if the alternatives are all members of the same recognized physical or chemical class or the same art-recognized class, and are disclosed in the specification or known in the art to be functionally equivalent and have a common use. Second, where a Markush grouping describes alternative chemical compounds, whether by words or chemical formulas, and the alternatives do not belong to a recognized class as set forth above, the members of the Markush grouping may be considered to share a "single structural similarity" and common use where the alternatives share both a substantial structural feature and a common use that flows from the substantial structural feature. See MPEP § 706.03(y).
The claims encompass a genus of genetically modified cells each capable of producing a genus of structurally and functionally unrelated products listed in a Markush group, wherein said genetically modified cells have genetic modifications that decrease the activity of functionally and structurally unrelated enzymes listed in a Markush group, or wherein said genetically modified cells have genetic modifications that increase the activity of functionally and structurally unrelated enzymes listed in a Markush group. These genetically modified cells would produce structurally and functionally unrelated products, and would have structurally and functionally unrelated genetic modifications.
The Markush grouping of products hexamethylenediamine (HMD), levulinic acid (LVA), 6-aminocaproic acid (6ACA), caprolactam (CPL), caprolactone (CPO), adipic acid (ADA), or 1,6-hexanediol (HDO) made by the cell in claims 1, 25, 61-65 (claims 54-60, 67, 161 dependent thereon) is improper because the alternatives defined by the Markush grouping do not share both a single structural similarity and a common use for the following reasons: each of these compounds have a different chemical structure and different function. For example, caprolactam has an N-containing ring, while adipic acid is a dicarboxylic acid that lacks rings and comprises a C4 chain. Therefore, there is not a single structural similarity or a common use.
The Markush grouping of genetic modifications that decrease the activity of the enzymes listed in part (a) of claim 1 (claims 25, 54-65, 67, 161 dependent thereon) is improper because the alternatives defined by the Markush grouping do not share both a single structural similarity and a common use for the following reasons: each of these modifications is made to decrease the activity of a genus of enzymes which are not structurally or functionally related. For example, an oxidoreductase is structurally and functionally different from a putrescine permease as these enzymes have different substrates, have different structures, and catalyze different reactions. Furthermore, modifications made to decrease the activity of an oxidoreductase are structurally and functionally unrelated to modifications made to decrease the activity of a putrescine permease, as these modifications are made to structurally and functionally unrelated enzymes that would have unrelated effects on the cell. Therefore, there is no single structural similarity or a common use.
The Markush grouping of genetic modifications that increase the activity of the enzymes listed in part (b) of claim 1 (claims 25, 54-65, 67, 161 dependent thereon) is improper because the alternatives defined by the Markush grouping do not share both a single structural similarity and a common use for the following reasons: each of these modifications is made to increase the activity of a genus of enzymes which are not structurally or functionally related. For example, an amidase is structurally and functionally different from a diamine permease as these enzymes have different substrates, have different structures, and catalyze different reactions. Furthermore, modifications made to increase the activity of an amidase are structurally and functionally unrelated to modifications made to increase the activity of a diamine permease, as these modifications are made to structurally and functionally unrelated enzymes that would have unrelated effects on the cell. Therefore, there is no single structural similarity or a common use.
The Markush grouping of byproducts listed in Table 10 or Table 11 as required in claims 25, 64-65 is improper because the alternatives defined by the Markush grouping do not share both a single structural similarity and a common use for the following reasons: each of Table 10 and Table 11 lists compounds (byproducts) that have different chemical structures and different functions. For example, Table 10 lists caprolactam, which has an N-containing ring, and also lists adipic acid, which is a dicarboxylic acid that lacks rings and comprises a C4 chain. Similarly, Table 11 lists acetate, which is a simple monocarboxylic acid containing two carbons, and also lists octanol, which is a primary alcohol that comprises eight carbons. Therefore, there is not a single structural similarity or a common use.
The Markush grouping of polyamides PA6, PA6,6, PA6,9, PA6,10, PA6,12 and PA6T listed in claim 59 is improper because the alternatives defined by the Markush grouping do not share both a single structural similarity and a common use for the following reasons: each of these polyamides comprise a different chemical structure and have a different function by virtue of their different structures. For example, polyamide 6 (PA6) is a polymer made by the polycondensation of caprolactam, which has an N-containing ring, while polyamide 66 (PA6,6; polyhexamethylene adipamide) is a polymer made by condensing hexamethylenediamine (C6 alkane-alpha,omega-diamine) with adipic acid (dicarboxylic acid), which are compounds that lack a ring. Therefore, there is not a single structural similarity or a common use.
The Markush grouping of pathways in Figures 1, 2, 3, 4, and 5 listed in claim 161 is improper because the alternatives defined by the Markush grouping do not share both a single structural similarity and a common use for the following reasons: each of the pathways listed in these figures are biosynthetic pathways for the production of compounds which are structurally and functionally unrelated. Moreover, these pathways require enzymes which themselves are structurally and functionally unrelated as they comprise different amino acid sequences, act on different substrates, and catalyze different reactions. For example, the pathway shown in Figure 4 from adipyl-CoA to hexanediol (HDO) requires the conversion of adipyl-CoA to adipate semialdehyde, adipate semialdehyde to 6-hydroxyhexanoate, 6-hydroxyhexanoate to 6-hydroxyhexanolyl-CoA, 6-hydroxyhexanolyl-CoA to 6-hydroxyhexanal, and 6-hydroxyhexanal to hexanediol), while the pathway shown in Figure 1 from succinyl-CoA and acetyl-CoA to levulinic acid requires the conversion of succinyl-CoA + acetyl-CoA to 3-oxoadipyl-CoA, 3-oxoadipyl-CoA to 3-oxoadipate, 3-oxoadipate to levulinic acid. Therefore, there is not a single structural similarity or a common use.
To overcome this rejection, Applicant may set forth each alternative (or grouping of patentably indistinct alternatives) within an improper Markush grouping in a series of independent or dependent claims and/or present convincing arguments that the group members recited in the alternative within a single claim in fact share a single structural similarity as well as a common use.
Claim Rejections - 35 USC § 112(b) or Second Paragraph (pre-AIA )
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, 25, 54-65, 67, 161 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 pre-AIA the applicant regards as the invention.
Claim 1 (claims 25, 54-65, 67, 161 dependent thereon) is indefinite in the recitation of “an oxidoreductase acting on an aldehyde or oxo moiety (A1)…” for the following reasons. It is unclear as to (i) whether the term in parentheses, (A1), intend to further limit the oxidoreductase, and if so, which is the limitation intended by the term “A1” to the oxidoreductase. For examination purposes, no patentable weight will be given to the term “(A1)”. Correction is required.
Claim 1 (claims 25, 54-65, 67, 161 dependent thereon) is indefinite in the recitation of “when compared to a cell without said one or more genetic modifications” for the following reasons. The claim does not require the comparison to be made with a cell of the same genus/species lacking the genetic modifications but rather allows for the comparison to be made with any cell lacking the genetic modifications. For example, as written, the comparison can be made between an E. coli cell having the genetic modifications and a wild type B. subtilis cell lacking the genetic modifications. The basis for comparison is variable, thus making the determination as to what is encompassed and not encompassed by the claim impossible. For example, cell X may be encompassed by the claim if the comparison is made with cell Y but may not be encompassed by the claim if the comparison is made with cell Z. For examination purposes, it will be assumed that the claim reads “when compared to the corresponding cell lacking the one or more genetic modifications”. Correction is required.
Claim 25 is indefinite in the recitation of “comprising a reduced level of one or more byproducts of Table 10 or Table 11” for the following reasons. As set forth in MPEP 2173.05(S), claims are to be complete in themselves and 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. In the instant case, the byproducts listed in these tables have a chemical name that can be recited in the claim. Correction is required.
Claim 56 is indefinite in the recitation of “wherein said byproduct increases the degradation of a polymer comprising said target product” for the following reasons. It appears that the limitation intends to limit the byproduct to a specific compound. However, in the absence of the conditions under which the degradation takes place, it is not possible to determine whether a byproduct is included or excluded from the scope of the claim. For example, the same byproduct can increase degradation of polymer X at pH Y and temperature Z and at the same time not increase degradation of polymer X if the pH is not Y and the temperature is not Z. Thus, the same byproduct can be included or excluded from the scope of the claim depending on the conditions used. For examination purposes, it will be assumed that claim 56 is a duplicate of claim 1. Correction is required.
Claims 57 and 60 (claims 58-59 dependent thereon) are indefinite in the recitation of “wherein said byproduct inhibits polymerization of target product to a polymer in a polymerization reaction” and “wherein said byproduct inhibits polymerization of …6ACA….in a polymerization reaction” for the following reasons. It appears that the limitations intend to limit the byproduct to a specific compound. However, in the absence of the conditions under which the polymerization inhibition takes place, it is not possible to determine whether a byproduct is included or excluded from the scope of the claims. For example, the same byproduct can inhibit the polymerization of target product X at pH Y and temperature Z and at the same time not inhibit polymerization of target product X if the pH is not Y and the temperature is not Z. For examination purposes, it will be assumed that claims 57-60 are duplicates of claim 1. Correction is required.
Claim 59 is indefinite in the recitation of “PA6”, “PA6,6”, “PA6,9”, “PA6,10”, “PA6,12” and “PA6T” for the following reasons. While it appears that these terms refer to a polyamide, the terms do not convey a particular structure/identity for the polyamide. If, for example, the term “PA6” refers to a polycaprolactam, the claim should be amended accordingly. For examination purposes, it will be assumed that the term “PA6” is equivalent to “polycaprolactam”. Correction is required.
Claims 61-63 are indefinite in the recitation of “greater than about” for the following reasons. The term “about” encompasses a range which includes values which are higher and lower than the recited reference value (e.g., 5 %, 99%). The term “greater than” implies that only values higher than the recited reference value are encompassed. Therefore, in the absence of a clear definition of what is encompassed by the term “about”, the term "greater than about" is unclear and confusing since the term refers to values which are higher than undefined values which are either higher or lower than the recited reference value. In essence, the term eliminates the relevance of the recited reference point because the reference value associated with “greater than” (e.g., 5 %, 99%) is variable and undefined. If the intended limitation is “greater than X%”, the claims should be amended accordingly. Correction is required.
Claim 61 is indefinite in the recitation of “in fermentation broth” for the following reasons. Claim 61 is directed to a cell. The limitation regarding the amount of target product in a fermentation broth can only be determined in a method that requires culturing a cell in a fermentation broth. Therefore, it is unclear as to how a limitation regarding the amount of a product in a fermentation broth can limit a cell. For examination purposes, claim 61 will be interpreted as a duplicate of claim 1. Correction is required.
Claims 62-63 are indefinite in the recitation of “…produces …..6ACA…that comprises….. 100%...6ACA …by weight after processing or purification” for the following reasons. The claims require a particular purity after purification. While this limitation appears to limit the cell, it is noted that purification is a step of a process and cannot further limit the cell, which is a product. The same cell X that produces Y amount of 6ACA can be encompassed and not encompassed by the claims depending on whether one uses purification method A or purification method B. If purification method A yields a product which is 100% 6ACA and purification method B yields a product which is 50% 6ACA, when the raw material used prior to purification comes from the same cell X, it would be impossible to determine whether cell X is encompassed or not by the claims. For examination purposes, claims 62-63 will be interpreted as duplicates of claim 1. Correction is required.
Claim 64 is indefinite in the recitation of “…produces …6ACA….that comprises less than ….1 ppm of one or more byproducts …..” for the following reasons. The term “ppm” or parts per million is a concentration unit. In the absence of a statement indicating which is the volume being used to determine such concentration (e.g., intracellular), it would be impossible to determine whether a cell is encompassed by the claim. For examination purposes, it will be assumed that claim 64 is a duplicate of claim 1.
Claims 64-65 are indefinite in the recitation of “one or more byproducts selected from Table 10 or Table 11” for the following reasons. As set forth in MPEP 2173.05(S), claims are to be complete in themselves and 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. In the instant case, the byproducts listed in these tables have a chemical name that can be recited in the claims. Correction is required.
Claim 67 is indefinite in the recitation of “….or 100% compared to a control cell lacking said genetic modification” for the following reasons. The term “a control cell” encompasses a genus of cells of any type. As such, the claim does not require the comparison to be made with a cell of the same genus/species lacking the genetic modifications but rather allows for the comparison to be made with any cell lacking the genetic modifications. For example, as written, the comparison can be made between an E. coli cell having the genetic modifications and a wild type B. subtilis cell lacking the genetic modifications. The basis for comparison is variable, thus making the determination as to what is encompassed and not encompassed by the claim impossible. For example, cell X may be encompassed by the claim if the comparison is made with cell Y but may not be encompassed by the claim if the comparison is made with cell Z. In addition, the term “lacking said genetic modification” is unclear because there is more than one genetic modification recited in claim 1. As such, one cannot determine which is the genetic modification that should be lacking in the “control cell”. For examination purposes, it will be assumed that claim 67 is a duplicate of claim 1. Correction is required.
Claim 161 is indefinite in the recitation of “wherein said cell comprises a target product pathway comprising a target product pathway comprising at least one exogenous nucleic acid encoding a target product pathway enzyme expressed in a sufficient amount to produce the target product, wherein said target product pathway comprises a pathway selected from Figure 1, 2, 3, 4 or 5” for the following reasons. As set forth in MPEP 2173.05(S), claims are to be complete in themselves and 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. In the instant case, the pathways shown in the figures are defined by the reactions encompassed by these pathways and can be incorporated in the claims by reciting the conversions encompassed by the pathways (e.g., levulinic acid pathway comprises the conversion of succinyl-CoA and acetyl-CoA to 3-oxoadipyl-CoA, the conversion of 3-oxoadipyl-CoA to 3-oxoadipate, and the conversion of 3-oxoadipate to levulinic acid). Correction is required.
When amending the claims, applicant is advised to carefully review all examined claims and make the necessary changes to ensure proper antecedent basis and dependency.
Claim Rejections - 35 USC § 112(a) or First Paragraph (pre-AIA )
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, 25, 54-65, 67, 161 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 pre-AIA the inventor(s), at the time the application was filed, had possession of the claimed invention.
As stated in MPEP 2111.01, during examination, the claims must be interpreted as broadly as their terms reasonably allow. Claims 1, 25, 54-65, 67, 161 are directed in part to a genus of genetically modified cells that have been modified by any means to produce 6-aminocaproic acid (6ACA), including the expression of a nucleic acid encoding an enzyme having any structure or function, wherein said cells have been further modified by any means to decrease the activity of a genus of enzymes having any structure, wherein said enzymes are oxidoreductases that act on an aldehyde or an oxo moiety, wherein said cells produce a reduced level of a genus of byproducts, including spermidine and octanol, compared to the level of byproducts produced in cells of the same genus and species lacking the genetic modifications. See Claim Rejections - 35 USC § 112(b) or Second Paragraph (pre-AIA ) for claim interpretation.
In University of California v. Eli Lilly & Co., 43 USPQ2d 1938, the Court of Appeals for the Federal Circuit has held that “A written description of an invention involving a chemical genus, like a description of a chemical species, ‘requires a precise definition, such as by structure, formula, [or] chemical name,’ of the claimed subject matter sufficient to distinguish it from other materials”. As indicated in MPEP § 2163, the written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice, reduction to drawings, or by disclosure of relevant, identifying characteristics, i.e., structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show that Applicant was in possession of the claimed genus. In addition, MPEP § 2163 states that 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.
The claims require a potentially large genus of (i) unknown modifications that can be made to any cell so that it can produce 6ACA, (ii) unknown nucleic acids encoding enzymes having any structure and function, wherein said enzymes are part of any 6ACA biosynthetic pathway, (iii) unknown modifications to decrease the activity of oxidoreductases acting on an aldehyde or oxo moiety, wherein said oxidoreductases have any structure, and (iv) unknown modifications to reduce the amount of byproducts, including reducing the amounts of spermidine and octanol. While the claims encompass the expression of a genus of genes encoding structurally and functionally unrelated enzymes, the specification is silent with regard to the structural features required in any gene that encodes an enzyme that could be used for the synthesis of 6ACA. Furthermore, while the claims require unknown modifications to decrease the activity of oxidoreductases acting on an aldehyde or oxo moiety, and the specification discloses the disruption of the endogenous E. coli yqhD and E. coli adhE genes, the specification is silent with regard to the structural features required in any endogenous gene encoding the required oxidoreductases. With regard to methods to reduce or increase the activity of an enzyme, while the specification discloses (a) disruption of a gene encoding the target enzyme as a method to reduce the activity of said enzyme, and (b) increasing the copy number of a gene encoding the desired enzyme, or using a strong heterologous promoter to express a gene encoding the desired enzyme, as methods to increase the activity of an enzyme, the specification is silent with regard to other genetic modifications that could be made to reduce/increase the activity of an enzyme, such as structural modifications to promoters, the expression of proteins that could act as inhibitors/enhancers of transcription, antisense molecules to block expression of the desired gene, or structural modifications to the coding region of a gene to alter the enzymatic activity of an enzyme. The specification fails to provide a structure/function correlation that would allow one of skill in the art to recognize those genes that encode the enzymes required by the claimed cells to produce 6ACA and the genetic modifications required in any cell to obtain the levels of byproducts recited.
A sufficient written description of a genus of genes/proteins may be achieved by a recitation of a representative number of genes/proteins defined by their nucleotide/amino acid sequence or a recitation of structural features common to members of the genus, which features constitute a substantial portion of the genus. However, in the instant case, there is no recited structural feature and there is no art-recognized correlation between structure and function which would provide those unknown structural features. In addition, while one could argue that sequences disclosed in the prior art are representative of the structure of all the members of the genus of genes/proteins required, it is noted that the art teaches several examples of differences in activity even when there is little structural variability. For example, Witkowski et al. (Biochemistry 38:11643-11650, 1999; cited in the IDS) teach that one conservative amino acid substitution transforms a β-ketoacyl synthase into a malonyl decarboxylase and completely eliminates β-ketoacyl synthase activity. Tang et al. (Phil Trans R Soc B 368:20120318, 1-10, 2013; cited in the IDS) teach that two Dehalobacter reductive dehalogenases, CfrA and DcrA, having 95.2% sequence identity to teach other have exclusively different substrate (Abstract; page 7, left column, Discussion, CfrA and DcrA). Seffernick et al. (J. Bacteriol. 183(8):2405-2410, 2001; cited in the IDS) teach that two naturally occurring Pseudomonas enzymes having 98% amino acid sequence identity catalyze two different reactions: deamination and dehalogenation, therefore having different function. Therefore, since minor structural differences may result in different function, and no additional information correlating structure with the desired activity has been provided, one cannot reasonably conclude that the genes/proteins of the prior art are representative of all the members of the genus of genes/proteins required to produce 6ACA in any cell with the level of byproducts required by the claims.
Due to the fact that the specification only discloses a very limited number of enzymes that can be used to produce 6ACA, a very limited number of modifications to increase or decrease the activity of an enzyme, and a single engineered organism (E. coli), which is able to produce 6ACA, one of skill in the art would not recognize from the disclosure that Applicant was in possession of the claimed invention.
Claims 1, 25, 54-65, 67, 161 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for an E. coli cell transformed with a nucleic acid encoding (i) a 3-oxoadipyl-CoA thiolase to catalyze the conversion of succinyl-CoA and acetyl-CoA to 3-oxoadipyl-CoA, (ii) a 3-oxoadipyl-CoA reductase to catalyze the conversion of 3-oxoadipyl-CoA to 3-hydroxyadipyl-CoA, (iii) a 3-hydroxyadipyl-CoA dehydratase to catalyze the conversion of 3-hydroxyadipyl-CoA to 5-carboxy-2-pentenoyl-CoA, (iv) a 5-carboxy-2-pentenoyl-CoA reductase to catalyze the conversion of 5-carboxy-2-pentenoyl-CoA to adipyl-CoA, (v) an adipyl-CoA reductase (aldehyde forming) to catalyze the conversion of adipyl-CoA to adipate semialdehyde, and (vi) a 6-aminocaproate transaminase and a 6-aminocaproate dehydrogenase to catalyze the conversion of adipate semialdehyde to 6ACA, wherein said E. coli cell has been further modified to disrupt the endogenous yqhD or adhE genes, does not reasonably provide enablement for a genetically modified cell that has been modified by any means to produce 6-aminocaproic acid (6ACA), including the expression of a nucleic acid encoding an enzyme having any structure or function, wherein said cell has been further modified by any means to decrease the activity of enzymes having any structure, wherein said enzymes are oxidoreductases that act on an aldehyde or an oxo moiety, wherein said cell produces a reduced level of byproducts, including spermidine and octanol, compared to the level of byproducts produced in a cell of the same genus and species lacking the genetic modifications. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention commensurate in scope with these claims.
Factors to be considered in determining whether undue experimentation is required are summarized in In re Wands (858 F.2d 731, 737, 8 USPQ2nd 1400 (Fed. Cir. 1988)) as follows: 1) quantity of experimentation necessary, 2) the amount of direction or guidance presented, 3) the presence and absence of working examples, 4) the nature of the invention, 5) the state of prior art, 6) the relative skill of those in the art, 7) the predictability or unpredictability of the art, and 8) the breadth of the claims. The factors that have led the Examiner to conclude that the specification fails to teach how to make and/or use the claimed invention without undue experimentation, are addressed in detail below.
The breadth of the claims. Claims 1, 25, 54-65, 67, 161 broadly encompass a genetically modified cell that has been modified by any means to produce 6-aminocaproic acid (6ACA), including the expression of a nucleic acid encoding an enzyme having any structure or function, wherein said cell has been further modified by any means to decrease the activity of enzymes having any structure, wherein said enzymes are oxidoreductases that act on an aldehyde or an oxo moiety, wherein said cell produces a reduced level of byproducts, including spermidine and octanol, compared to the level of byproducts produced in a cell of the same genus and species lacking the genetic modifications. See Claim Rejections - 35 USC § 112(b) or Second Paragraph (pre-AIA ) for claim interpretation.
The enablement provided is not commensurate in scope with the claims due to the large number of unknown modifications one could make to any cell so that it can produce 6ACA, the large number of unknown genes encoding enzymes that could be used to produce 6ACA in any cell, the large number of unknown modifications one could make to decrease/increase the activity of an enzyme, and the large number of unknown modifications one could make to decrease byproducts, such as spermidine and octanol, as recited in the claims. In the instant case, the specification enables an E. coli cell transformed with a nucleic acid encoding (i) a 3-oxoadipyl-CoA thiolase to catalyze the conversion of succinyl-CoA and acetyl-CoA to 3-oxoadipyl-CoA, (ii) a 3-oxoadipyl-CoA reductase to catalyze the conversion of 3-oxoadipyl-CoA to 3-hydroxyadipyl-CoA, (iii) a 3-hydroxyadipyl-CoA dehydratase to catalyze the conversion of 3-hydroxyadipyl-CoA to 5-carboxy-2-pentenoyl-CoA, (iv) a 5-carboxy-2-pentenoyl-CoA reductase to catalyze the conversion of 5-carboxy-2-pentenoyl-CoA to adipyl-CoA, (v) an adipyl-CoA reductase (aldehyde forming) to catalyze the conversion of adipyl-CoA to adipate semialdehyde, and (vi) a 6-aminocaproate transaminase and a 6-aminocaproate dehydrogenase to catalyze the conversion of adipate semialdehyde to 6ACA, wherein said E. coli cell has been further modified to disrupt the endogenous yqhD or adhE genes.
The amount of direction or guidance presented and the existence of working examples. The specification discloses an E. coli genetically modified to express nucleic acids encoding (i) a 3-oxoadipyl-CoA thiolase to catalyze the conversion of succinyl-CoA and acetyl-CoA to 3-oxoadipyl-CoA, (ii) a 3-oxoadipyl-CoA reductase to catalyze the conversion of 3-oxoadipyl-CoA to 3-hydroxyadipyl-CoA, (iii) a 3-hydroxyadipyl-CoA dehydratase to catalyze the conversion of 3-hydroxyadipyl-CoA to 5-carboxy-2-pentenoyl-CoA, (iv) a 5-carboxy-2-pentenoyl-CoA reductase to catalyze the conversion of 5-carboxy-2-pentenoyl-CoA to adipyl-CoA, (v) an adipyl-CoA reductase (aldehyde forming) to catalyze the conversion of adipyl-CoA to adipate semialdehyde, and (vi) a 6-aminocaproate transaminase and a 6-aminocaproate dehydrogenase to catalyze the conversion of adipate semialdehyde to 6ACA. The specification also discloses disruption of the endogenous yqhD and/or adhE genes which encode oxidoreductases that act on an aldehyde. However, the specification fails to disclose (i) other genetic modifications to produce 6ACA, (ii) the structure and/or identity of additional genes which encode enzymes that can be used for the synthesis of 6ACA, (iii) the structure of other oxidoreductases acting on an aldehyde or oxo moiety, (iv) other genetic modifications to increase/decrease enzymatic activity, or (v) other modifications to decrease the level of bioproducts. No structure/function correlation has been provided that would allow one of skill in the art to determine those genes that encode the recited enzymes, or the structural modifications that can be made to any cell that would result in the desired byproduct levels.
The state of prior art, the relative skill of those in the art, and the predictability or unpredictability of the art. The amino acid sequence of a protein determines the function of such protein. Neither the specification nor the art provide a correlation between structure and function such that one of skill in the art can envision the structure of any protein (or its gene) that could be used to synthesize 6ACA, or the structure of any oxidoreductase as required by the claims. In addition, the art does not provide any teaching or guidance as to which genetic modifications can be made to any cell so that any of the byproducts required by the claims, including spermidine and octanol, can be reduced. The art provides no guidance as to any additional methods to increase/reduce the activity of the recited enzymes that do not require some knowledge or guidance as to the structural features of the enzymes or their coding genes.
While the argument can be made that the structure/identity of those enzymes and their corresponding genes can be obtained by structural homology, the art clearly teaches that (i) there is a high level of unpredictability associated with accurate functional annotation of proteins based solely on structural homology, and (ii) modification of a protein’s amino acid sequence to obtain the desired activity without any guidance/knowledge as to which amino acids in a protein are tolerant of modification and which ones are conserved is highly unpredictable. For example, Singh et al. (Current Protein and Peptide Science 19(1):5-15, 2018) disclose different protein engineering approaches and state that despite the availability of an ever-growing database of protein structures and highly sophisticated computational algorithms, protein engineering is still limited by the incomplete understanding of protein functions, folding, flexibility and conformational changes (page 11, left column, last paragraph). Sadowski et al. (Current Opinion in Structural Biology 19:357-362, 2009; cited in the IDS) teach that much of the problem in assigning function from structure comes from functional convergence, where although a stable structure is required to perform many functions it is not always necessary to adopt a particular structure to carry out a particular function (page 357, right column, first full paragraph). Sadowski et al. further explain that the unexpected and significant difficulties of predicting function from structure show that the potential of structural models for providing novel functional annotations has not yet fully realized. Sadowski et al. also states that while a few successes have been achieved which required manual intervention, the ability to vary the requirements for specificity in prediction means that it is difficult to determine how useful the end result may be for the user (page 361, left column, first full paragraph). The teachings of Singh et al. and Sadowski et al. are further supported by the teachings of Witkowski et al., Tang et al. and Seffernick et al. already discussed above, where it is shown that even small amino acid changes result in enzymatic activity changes.
The quantity of experimentation required to practice the claimed invention based on the teachings of the specification. While methods of isolating polypeptides and genes were known in the art at the time of the invention, it was not routine in the art to screen by a trial and error process for an infinite number of proteins/genes and determine which ones have the desired enzymatic activity or encode a protein with the desired enzymatic activity. Similarly, it was not routine in the art to screen by a trial and error process for an infinite number of genetic modifications, proteins that can act as expression regulators, or antisense molecules that could block expression of the desired genes. In the absence of (a) a rational and predictable scheme for identifying which proteins and their genes are more likely to have the desired activity, (b) a correlation between structure and activity, (c) a rational and predictable scheme for identifying those genetic modifications most likely to result in a reduction of byproduct formation, and (d) some knowledge or guidance as to which genetic modifications can result in decrease/increase enzymatic activity in any cell, one of skill in the art would have to test an essentially infinite number of proteins, nucleic acids, and modifications to determine which genetic modifications would lead to the desired outcome, and which proteins have the desired activity.
Therefore, taking into consideration the extremely broad scope of the claims, the lack of guidance, the amount of information provided, the lack of knowledge about a correlation between structure and function, and the high degree of unpredictability of the prior art in regard to function determination based on structural homology, one of ordinary skill in the art would have to go through the burden of undue experimentation in order to practice the claimed invention. Thus, Applicant has not provided sufficient guidance to enable one of ordinary skill in the art to make and use the invention in a manner reasonably correlated with the scope of the claims.
Claim Rejections - 35 USC § 102 (AIA )
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, 25, 54-65, 67, 161 are rejected under 35 U.S.C. 102(a)(1) and 102(a)(2) as being anticipated by Lau et al. (US Publication No. 2013/0288320, publication date 10/31/2013; cited in the IDS).
Claims 1, 25, 54-65, 67 and 161 are directed in part to a cell that produces 6ACA, wherein said cell has been genetically modified to express at least one exogenous nucleic acid encoding an enzyme of a 6ACA biosynthetic pathway, wherein said cell comprises a disruption in an endogenous gene encoding an oxidoreductase acting on an aldehyde, wherein said cell produces a reduced amount of a byproduct compared to the corresponding cell that lacks the genetic modifications, wherein said byproduct is one of Table 10, such as 6-hydroxyhexanoate (By 15). See Claim Rejections - 35 USC § 112(b) or Second Paragraph (pre-AIA ) for claim interpretation.
Lau et al. teach a genetically modified organism that produces 6-amino caproic acid (6ACA; paragraph [0024], [0071]). Lau et al. teach E. coli as one of the genetically modified organisms (paragraph [0031]). Lau et al. teach that the genetically modified organism is made by transforming the host cell with at least one polynucleotide encoding an enzyme involved in the engineered metabolic pathway (paragraph [0032]). Lau et al. teach that the production of 6-hydroxyhexanoate (6HH) from adipate semialdehyde is catalyzed by an alcohol dehydrogenase from EC 1.1.1.1, specifically those acting on the CH-OH group (aldehyde; paragraph [0098]). Lau et al. teach that the cell can be genetically modified to knock out genes to reduce byproduct formation, such as the adhE gene (paragraph [0095]). As indicated in the specification, the adhE gene encodes an oxidoreductase that belongs to EC 1.1.1.1 where the substrate functional group is an aldehyde (Table 3; A2 and A4). Since the enzyme encoded by the adhE gene catalyzes the synthesis of 6HH from adipate semialdehyde, it follows that the genetically modified cell that has a disruption in the endogenous adhE would have a reduced formation of 6HH compared to wild type E. coli. Therefore, the E. coli cell of Lau et al. anticipates the instant claims as written/interpreted.
Claims 1, 25, 54-65, 67, 161 are rejected under 35 U.S.C. 102(a)(1) and 102(a)(2) as being anticipated by Burk et al. (U.S. Patent No. 8,377,680, issued 2/19/2013; cited in the IDS) as evidenced by Dittrich et al. (Biotechnology Progress 21:1062-1067, 2005).
Claims 1, 25, 54-65, 67 and 161 are directed in part to a cell that produces 6ACA, wherein said cell has been genetically modified to express at least one exogenous nucleic acid encoding an enzyme of a 6ACA biosynthetic pathway, wherein said cell comprises a disruption in an endogenous gene encoding an oxidoreductase acting on an aldehyde, wherein said cell produces a reduced amount of a byproduct compared to the corresponding cell that lacks the genetic modifi