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 of Group I (claims 1-11) and species of SEQ ID NO: 6 (MHETase), E. aphidicola, and PET in the reply filed on 06/18/2026 is acknowledged. Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.01(a)). While applicant states “with traverse,” there is a failure to distinctly and specifically point out the supposed errors in the restriction requirement.
Claims 12-23 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected Invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 06/18/2026.
Drawings
The drawings are objected to because 37 CFR 1.84(l) requires every line, number, and letter must be durable, clean, black (except for color drawings), sufficiently dense and dark, and uniformly thick and well-defined. Fig. 2 (chemical structures) and Figs 4-6, 9-10, 12-14 and 20 have small, illegible or blurry text including chemical structures that cannot be discerned or reproduced.
Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Specification
The disclosure is objected to because of the following informalities:
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01. See page 36.
Appropriate correction is required.
Claim Objections
Claim 9 is objected to because of the following informalities:
In claim 9, Wt% as recited is not a proper unit for a ratio by weight as recited. Weight ratios are not defined by reference to a base of 100 as a percentage. For example, a weight ratio of 50:50, 1:1, 2:2, and 10:10 are all the same weight ratio. That is, a weight ratio is a unitless relationship not defined as a wt% such that “wt%” should be removed from claim 9.
Appropriate correction is required.
Claim Interpretation
MPEP 2173.05(b)(III)(E) provides the following guidance:
The addition of the word "type" to an otherwise definite expression (e.g., Friedel-Crafts catalyst) extends the scope of the expression so as to render it indefinite. Ex parte Copenhaver, 109 USPQ 118 (Bd. Pat. App. & Inter. 1955). Likewise, the phrase "ZSM-5-type aluminosilicate zeolites" was held to be indefinite because it was unclear what "type" was intended to convey.
The claim terms PETase-like and MHETase-like are not considered to be indefinite since the enzymatic activity required is expressly set forth in claim 1 and applicant is otherwise allowed to be their own lexicographer. These enzymes are referenced as PETase and MHETase below without the -like modifier.
Claim Rejections - 35 USC § 103
Claim(s) 1-3, 5, 7 and 10-11 is/are rejected under 35 U.S.C. 103 as being unpatentable over Beckham et al. (U.S. 2021/0180007 A1) (see IDS) further in view of Sulaiman et al. (Isolation of a Novel Cutinase Homolog with Polyethylene Terephthalate-Degrading Activity from Leaf-Branch Compost by Using a Metagenomic Approach, Appl. Environ. Microbiol. 78, 2012, 1556-62) and GenBank, Accession No., HQ704839, 2012, www.ncbi.nlm.nih.gov (previously cited).
Beckham, abstract, teaches:
Disclosed herein are engineered P. putida KT2440 co-expressing PETase and MHETase enzymes that selectively degrades PET into monomers, ethylene glycol and terephthalate (TPA). In another embodiment, disclosed herein are methods for making and using a highly efficient EG metabolizing P. putida KT2440 strain. Given that native P. putida does not have a TPA metabolic pathway, nor the proteins to transport TPA into the cell, the next metabolic engineering challenge for developing synthetic P. putida strain to plastic upcycling was enabling TPA catabolism in P. putida KT2440. TPA transporters and catabolic pathway have been characterized in several microorganisms including Comamonas sp. strain E6 and Rhodococcus jostii RHA1.
“The present disclosure also relates to a biological strategy for degrading PET, which can subsequently enable atom-efficient biological transformations to novel intermediates (e.g., β-ketoadipate and/or muconate), which may be converted to high strength composites. PETase hydrolyses PET to produce bis(2-hydroxyethyl) terephthalate (BHET), mono-(2-hydroxyethyl) terephthalate (MHET), terephthalate (TPA), and ethylene glycol (EG), and MHETase catalyzes MHET to TPA [terephthalic acid] and EG. Hence, as shown herein, co-expression of PETase and MHETase in an engineered strain can enable PET degradation to TPA and EG. Thus, in some embodiments of the present disclosure, a biological method is provided for the selective degradation of PET into PET monomers via co-expression and secretion of PETase and MHETase in Pseudomonas putida, which can grow well in simple minimal salt medium.” Beckham, para. [0039].
“FIG. 9 depicts the amino acid sequences of PETase (SEQ ID NO: 4) and MHETase (SEQ ID NO: 5).” Beckham, para. [0021].
SEQ ID NO: 5 of Beckham is over 85% identical to recited SEQ ID NO: 6, wherein SEQ ID NO: 5 of Beckham is an exemplary MHETase of Beckham. Beckham, para. [0021].
“Among other things, I. sakaiensis PETase, ISF6_4831 and MHETase, ISF6_0224 genes were codon optimized for expression in KT2440 including their secretion signal peptides, which are compatible to the P. putida chaperone SecB-dependent secretion system.” Beckham, para. [0040]. That is, Beckham explains that any heterologous PETase or MHETase encoding genes (i.e. heterologous DNA) consistent with the teachings of Beckham is described as including a secretion signal peptide liked (i.e. linked in frame) to any expressed and secreted PETase and MHETase.
However, Beckham does not describe the PETase as having at least 85% identity to recited SEQ ID NO: 5.
Beckham, claim 1, recites a genetically modified microorganism expressing any PETase such that embodiments of Beckham are not limited to specific PETase species described therein. Sulaiman, abstract, teaches “LC-cutinase* had an ability to degrade poly(-caprolactone) and polyethylene terephthalate (PET). The specific PET-degrading activity of LC-cutinase* was determined to be 12 mg/h/mg of enzyme (2.7mg/h/ katofpNP-butyrate-degrading activity) at pH 8.0 and 50°C. This activity is higher than those of the bacterial and fungal cutinases reported thus far, suggesting that LC-cutinase* not only serves as a good model for understanding the molecular mechanism of PET-degrading enzyme but also is potentially applicable for surface modification and degradation of PET.”
Suliman, page 1560, right col., states:
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This is understood as describing activity to of degrading BHET into MHET, and a PETase having the same function to degrade PET to TPA and ethylene glycol as taught in Beckham, abstract. That is, the cutinase taught by Sulaiman is by definition of PETase is the same has activity to convert PET to TPA and MHET. Beckham, para. [0039], sets forth that PETase activity is understood in the art as converting PET to final TPA, EG and MHET degradation products at least in part through a BHET intermediate that is degraded by the cutinase and therefore not detected. The description in Suliman that BHET was not detected is understood that BHET was broken down to TPA and EG by the described LC-cutinase.
“The nucleotide sequence of the LC-cutinase gene has been deposited in GenBank under accession number HQ704839. Sulaiman, page 1558, left col. The protein sequence shown in GenBank HQ704839 has over 85% identity to recited SEQ ID NO: 5.
That is, the “cutinase” taught by Sulaiman is a PETase and within the broadest reasonable definition of a PETase-like enzyme that is particularly suitable for degradation of PET. As such, at the time of filing an ordinarily skilled artisan would have been motivated to form embodiments of claim 1 of Beckham wherein the PETase enzyme is the LC cutinase enzyme taught by Sulaiman, since the same is a particularly effective PETase, Claim 5 of Beckham further teaches that heterologous PETase or MHETase genes be linked to a secretion signal polypeptide such that upon formation of Beckham wherein MHETase is SEQ ID NO: 5 of Beckham and PETase is LC cutinase of Suliman, the features of at least claims 1 and 2.
Regarding claim 3, Sulaiman, abstract, describes the cutinase/PETase described therein as having an optimal pH of 8 or 8.5 and optimal temperature of 50[Symbol font/0xB0]C as to have activity at a pH and temperature falling within the ranges recited in claim 3. “As shown in Fig. S4 in the supplemental material, LCcutinase* lost activity with half-lives of 5 h at 50°C, 80 min at 60°C, 40 min at 70°C, and 7 min at 80°C.” Sulaiman, page 1560, left col. The temperature dependence of LC-cutinase* was analyzed at various temperatures ranging from 30 to 80°C and pH 7.0 (sodium phosphate) using pNP-butyrate as a substrate. LCcutinase* exhibited the highest activity at 50°C (specific activity of 3.2 +/- 0.35 ukat/mg) and roughly 70% of the maximal activity at 30 and 70°C. Sulaiman, Fig. S3 shows that the described cutinase/PETase has activity over the whole range of 25-80[Symbol font/0xB0]C and over the whole pH range of 6-9. The preceding is understood as falling within the broadest reasonable interpretation of thermostable and as evidence that the cutinase/PETase has some minimal activity at the pH and temperatures recited in claim 3.
Regarding claim 5, Table 2 of Beckham describes a plasmid pLJ080 PETase and MHETase, wherein Fig. 7 of Beckham shows the same Ptac-promoter controlling expression of both PETase and MHETase genes. As such, in embodiments consistent with the teachings of Beckham wherein the PETase as taught by Sulaiman is employed, an ordinarily skilled artisan at time of filing would have been motivated to express PETase and MHETase in the same manner as taught by Beckham being co-expression from one plasmid under control of a single promoter.
Regarding claim 7, the above description of Sulaiman indicates that the PETase (cutinase) is enzymatically at 30[Symbol font/0xB0]C. Beckham, para. [0049], describes a PET and BHET degradation experiment wherein the MHETase enzyme is employed at a temperature of 30[Symbol font/0xB0]C. “Cultures were incubated shaking at 225 rpm, 30° C. 1 mL samples were collected periodically and subjected to HPLC analysis to detect the degraded products. After the fermentation, PET coupons were subjected to microscopic observation.” Beckham, para. [0049]. As such, the MHETase enzyme described by Sulaiman also has apparent enzymatic activity at 30[Symbol font/0xB0]C.
Regarding claim 10, Beckham, para. [0049], as discussed above further teaches the features of claim 10: “To assess the selective degradation of PET/BHET by the PETase and MHETase expressing strain, shake flask experiments were performed using 125 mL baffled flasks containing 25 mL modified M9 media (6.78 g/L Na2HPO4, 3.00 g/L K2HPO4, 0.50 g/L NaCl, 1.66 g/L NH4Cl, 0.24 g/L MgSO4, 0.01 g/L CaCl2, and 0.002 g/L FeSO4) supplemented with 20 mM of glucose and amorphous PET coupons (amorphous PET films with a crystallinity of 14.8±0.2%, synthesized at NREL) or BHET (Obtained from IBM Almaden Research Center, BHET was derived from waste PET bottles via chemical depolymerization process), and inoculated to OD600 0.1 with pre-culture. Pre-cultures of the strains were prepared by inoculating 25 mL M9 medium supplemented with 20 mM glucose in a 125 mL baffled flask to an OD600 of 0.05-0.1 and incubating shaking at 225 rpm, 30° C. At mid log phase (OD600 0.5-1.0) cells were harvested by centrifugation at 13,000 rpm, and the cell pellets were washed twice and resuspended in M9 medium without a carbon source. Cultures were incubated shaking at 225 rpm, 30° C. 1 mL samples were collected periodically and subjected to HPLC analysis to detect the degraded products.” The supplemented M9 media is culturing the recombinant bacterial cell in a liquid medium wherein as discussed above it is understood that any expressed PETase or MHETase is secreted. As such, the collected “1 mL samples were collected periodically and subjected to HPLC analysis to detect the degraded products” contain the PETase and MHETase enzymes in addition to degradation products.
Further regarding claims 10 and 11, Sulaiman, page 1557, right col., teaches production of the PETase/cutinase described therein by a recombinant E. coli expressing a heterologous DNA encoding the same as follows:
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As such, Sulaiman teaches that wherein a recombinant cell expresses and secretes a protein of interest, which includes a PETase as taught by Sulaiman or such a PETase combined with a MHETase, that it is known that such a recombinant cell can be cultured in an appropriate liquid medium wherein the enzymes will be secreted, and the liquid medium (i.e. a bacterial culture) can be collected by centrifugation to produce a supernatant and a cell pellet wherein the supernatant can be collected containing the enzymes of interest, which are PETase and MHETase as discussed. That is, while Sulaiman teaches a recombinant E. coli secreted and enzyme of interest and Beckham in view of the teachings of Sulaiman teaches a recombinant P. putida expressing and secreting PETase and MHETase as recited in claim 1, Sulaiman teaches and motivates an ordinarily skilled artisan at time of filing that any recombinant bacterium expressing and secreting an enzyme of interest can have such an enzyme advantageously recovered by performing the method steps recited in claims 10 and 11, which extends to a P. putida bacterium cell expressing and secreting a PETase and MHETase as recited in claim 1.
Claim(s) 1-5, 7 and 10-11 is/are rejected under 35 U.S.C. 103 as being unpatentable over Beckham et al. (U.S. 2021/0180007 A1) (see IDS) further in view of Sulaiman et al. (Isolation of a Novel Cutinase Homolog with Polyethylene Terephthalate-Degrading Activity from Leaf-Branch Compost by Using a Metagenomic Approach, Appl. Environ. Microbiol. 78, 2012, 1556-62) and GenBank, Accession No., HQ704839, 2012, www.ncbi.nlm.nih.gov as applied to claims 1-3, 5, 7 and 10-11 above, and further in view of Sathesh-Prabu et al. (Inducible and tunable gene expression systems for Pseudomonas putida KT2440, Sci. Reports, 10 Sept. 2021, 118079).
Regarding claim 4, Beckham indicates the use of a constitutive promoter for expression. See Beckham, para. [0042]. Sathesh-Prabu, page 1, teaches:
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Substitution of known elements is obvious upon a finding of:
(1) a finding that the prior art contained a device (method, product, etc.) which differed from the claimed device by the substitution of some components (step, element, etc.) with other components;
(2) a finding that the substituted components and their functions were known in the art;
(3) a finding that one of ordinary skill in the art could have substituted one known element for another, and the results of the substitution would have been predictable; and
(4) whatever additional findings based on the Graham factual inquiries may be necessary, in view of the facts of the case under consideration, to explain a conclusion of obviousness. (MPEP 2143(I)(B)).
As discussed, Beckham teaches use of a constitutive promoter. However, the prior art of Sathesh-Prabu teaches that multiple types of inducible promoters are known in the prior art for use in P. putida KT2440 including inducible promoter suitable for “industrial scale-up” wherein the degradation of PET taught by Beckham is understood as relating to a process applicable to be employed in industrial scale for addressing PET waste. Both constitutive and inducible promoters serve the function of allowing for expression of heterologous genes in P. putida wherein a person having ordinarily skill in the art at time of filing could have substituted a constitutive promoter for an inducible promoter as taught by Sathesh-Prabu with predictability in expressing heterologous genes after application of an appropriate induction condition. No additional findings are deemed to be particularly necessary to explain a conclusion of obviousness. As such, in view of the guidance of MPEP 2143(I)(B), an ordinarily skilled artisan at time of filing would have been motivated to substitute a constitutive promoter as taught by Beckham with an inducible promoter as taught by Sathesh-Prabu.
Claim(s) 1-3, 5, and 7-11 is/are rejected under 35 U.S.C. 103 as being unpatentable over Beckham et al. (U.S. 2021/0180007 A1) (see IDS) further in view of Sulaiman et al. (Isolation of a Novel Cutinase Homolog with Polyethylene Terephthalate-Degrading Activity from Leaf-Branch Compost by Using a Metagenomic Approach, Appl. Environ. Microbiol. 78, 2012, 1556-62) and GenBank, Accession No., HQ704839, 2012, www.ncbi.nlm.nih.gov as applied to claims 1-3, 5, 7 and 10-11 above, and further in view of Li (Plastic monomer degradation Engineering Pseudomonas putida KT2440 for plastic monomer utilization, 2020, Diss. RWTH Aachen University).
Regarding claims 8 and 9, the broadest reasonable interpretation of claims 8 and 9 do not require 1) the recited recombinant bacterial cell to be present in any composition containing biomass, PET or degradation products of PET from ODH treatment of the same, or 2) performance of any step of a method including any active step of an OHD process. Rather, claims 8 and 9 only require the bacterial cell to be latently “capable of growing” [i.e. no active step of growing required] on a substrate containing biomass (e.g. coffee, tea) co-mixed with PET pretreated in an OHD process” including such substrate having a ratio of PET to biomass by weight from 1:99 to 50:50. Further, such “capable of growing” does not exclude the presence of other materials in addition to pretreated PET and biomass, for example glucose. While the claims can be amended to recite a composition containing the recombinant bacterial cell and degradation products produced by an OHD process, the claims do not presently recite such a composition and the rejections below are therefore do not address such a composition. Rather, a complete embodiment of claims 8 and 9 is an isolated recombinant bacterial cell meeting the limitations of the claims with no other compound present.
With the above in mind, P. putida having resistance to the degradation products of PET are known in the prior art. First, Beckham, para. [0016], teach “FIG. 4 depicts Engineered TPA [terephthalic acid] catabolic pathway in P. putida KT2440, transporter TpaK and catabolic genes (TphA1, TphA2, TphA3, and TphB) are originally from R. jostii RHA1 and Comamonas sp. strain E6, respectively,” such that the described P. putida can utilize TPA degradation product of PET as an energy and carbon source for the cell. “FIG. 5 depicts Engineered P. putida KT2440 strain enables TPA utilization. (A) Growth curves of the strain (B) growth rate of the strains (C) TPA utilization of the strains. Growth of the strains was assessed in minimal medium containing either 10 mM TPA or 10 mM PCA as the sole substrate for growth, and TPA utilization was measured during growth in minimal medium with 10 mM TPA as the sole growth substrate.” Beckham, para. [0017]. The preceding is understood as a description of T. putida consistent with the teachings of Beckham being able to grow on TPA as a sole carbon source.
Second, Li, abstract, teaches:
aiming for a biotechnological
conversion of plastic waste like PET and PU. These polymers can be hydrolysed by enzymes,
releasing monomers like ethylene glycol (EG), 1,4-butanediol (BDO), and adipic
acid (AA). These can be utilized as carbon source by microorganisms like the biotechnological
workhorse Pseudomonas putida KT2440 to produce value-added compounds
from plastic waste.
This thesis enabled P. putida KT2440 to efficiently metabolize the plastic monomers EG,
BDO, and AA. Since P. putida KT2440 is not able to grow on EG, adaptive laboratory
evolution (ALE) was performed to isolate the enhanced mutants. Genome resequencing
and reverse engineering revealed that the deletion of one regulator, gclR, was sufficient
to enable growth on EG. The deletion of two additionally identified genes, PP_2046
and PP_2662, could further enhance this growth. With this knowledge, EG metabolism
and its regulation in P. putida was further unraveled.
Li, page 46, further states: we could demonstrate that glycolaldehyde and glyoxal are indeed toxic to cells of P. putida KT2440 in concentrations above 4 mM, and that preventing the accumulation of these intermediates during ethylene glycol metabolism is crucial for efficient growth.
As discussed, Beckham teaches a P. putida engineered with a TPA catabolism pathway. Li teaches that P. putid can further be engineered to utilize and/or have resistance to additional degradation products of PET including ethylene glycol. As discussed by Beckham, abstract, the combined activities of PETase and MHETase converts PET to TPA and ethylene glycol. As such, at the time of filing, an ordinarily skilled artisan at time of filing would have been motivated in addition to a TPA catabolism pathway, for the P. putida consistent with the teachings of Beckham to further have modifications to allow for ethylene glycol as well to allow for the benefit of cell growth on the products of PET hydrolysis being TPA and ethylene glycol.
"In relying upon the theory of inherency, the examiner must provide a basis in fact and/or technical reasoning to reasonably support the determination that the allegedly inherent characteristic necessarily flows from the teachings of the applied prior art." MPEP 2112(IV).
The specification describes the following:
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Example 5 of the specification is an OHD process performed on biomass (Tea/coffee/corn stover) mixed with PET. As such, the specification is understood as describing that wild-type P. putida KT2440 is able to grow in the presence of a substrate containing biomass (e.g. tea/coffee/corn stover) and PET pretreated by an OHD process as recited in claims 8 and 9, wherein Fig. 12 shows data produced by wild-type P. putida KT2440 including wherein a ratio of PET to biomass by weight is from 1:99 to 50:50. While Example 8 of the specification does not appear to show any data result from “using Mplex reader . . . to monitor the growth,” it appears that wild-type P. putida KT2440 is able to grow in the presence of a substrate containing biomass (e.g. tea/coffee/corn stover) and PET pretreated by an OHD process as recited in claims 8 and 9, including a ratio of PET to biomass by weight from 1:99 to 50:50 wt%.
The evidence of record that wild-type P. putida KT2440 is able to grow in the presence of a substrate containing biomass (e.g. tea/coffee/corn stover) and PET pretreated by an OHD process (including at a ratio of PET to biomass by weight from 1:99 to 50:50 wt%) as recited in claims 8 and 9 supports a reasonable conclusion that a P. putida KT2440 engineered to be able to catabolize TPA and/or ethylene glycol as taught by Beckham and Li and further expressing PETase and MHETase as discussed above maintains such ability to grow in the presence of a substrate containing biomass (e.g. tea/coffee/corn stover) and PET pretreated by an OHD process. That is, among the many degradation products produce by an OHD process applied to a mix of biomass (e.g. corn stover) and PET (including at a ratio of PET to biomass by weight from 1:99 to 50:50 wt%) would be expected to be TPA, ethylene glycol, BHET and MHET which are utilized by such P. putida able to catabolize TPA and/or ethylene glycol and expressing PETase and MHETase such that the evidence of record would indicate that such modified P. putida would be able to better grow on the presence of a substrate containing biomass (e.g. tea/coffee/corn stover) and PET pretreated by an OHD process (including at a ratio of PET to biomass by weight from 1:99 to 50:50 wt%) than wild-type P. putida KT2440 apparently having an ability to grow on such an OHD-pretreated substrate.
Allowable Subject Matter
Claim 6 is objected to as being dependent upon a rejected base claim, but would be allowable if rewritten in independent form including all of the limitations of the base claim and any intervening claims.
The following is a statement of reasons for the indication of allowable subject matter: SEQ ID NO: 4 is an enzyme found in Erwinia and is associated with gene name catB. Deletion of catB gene in host cells to promote muconic acid production is known in the art. For example, Van Duuren et al. (EP 2562249 A1), claims 1-6 and para [0002], describe P. putida KT2440 having catB gene deletion, wherein Erwinia is mentioned briefly in para. [0024].
Regardless, there is not deemed to be sufficient motivation in the prior art to combine the specific modification of SEQ ID NO: 4 in an Erwinia host cell in combination with PETase and MHETase expression as required in claim 6. It is noted that subject matter highly similar to claim 6 is described in Dissanayake et al. (A catabolic powerhouse for biorefineries, Trends Biotechnol., 2026, doi.org/10.1016/j.tibtech.2026.03.022), see Fig. 4 and related text.
Conclusion
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/TODD M EPSTEIN/Primary Examiner, Art Unit 1652
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