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 .
Requirement for Information
Applicant and the assignee of this application are required under 37 CFR 1.105 to provide the following information that the examiner has determined is reasonably necessary to the examination of this application.
In response to this requirement, please provide answers to each of the following interrogatories eliciting factual information:
The specification, para. [0036], describes the following:
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Is the referenced “novel Pseudomonas putida” a naturally-occurring microorganism or is it artificially produced?
If the novel P. putida is a naturally-occurring microorganism, is the gene having recited SEQ ID NO: 1 a naturally-occurring gene in the genome of the same, and is the omega-transaminase having recited SEQ ID NO: 2 produced by such novel P. putida?
The applicant is reminded that the reply to this requirement must be made with candor and good faith under 37 CFR 1.56. Where the applicant does not have or cannot readily obtain an item of required information, a statement that the item is unknown or cannot be readily obtained may be accepted as a complete reply to the requirement for that item.
This requirement is an attachment of the enclosed Office action. A complete reply to the enclosed Office action must include a complete reply to this requirement. The time period for reply to this requirement coincides with the time period for reply to the enclosed Office action.
Claim Objections
Claim 3 is objected to because of the following informalities:
In claim 3 (line 4), “the Pseudomonas putida ω-transaminase gene” is considered to have inherent antecedent basis in “expressing a Pseudomonas putida ω-transaminase in a host cell.” However, the claim should be placed in better form by providing an explicit antecedent basis for “the Pseudomonas putida ω-transaminase gene” in claim 3. Further in claim 3 (line 3), claim 3 should recite “a crude enzyme solution, a crude enzyme powder, or a pure enzyme.”
Appropriate correction is required.
Specification
The disclosure is objected to because of the following informalities:
The use of the term pCold™, BL21 Star™ and SHuffle®, which is a trade name or a mark used in commerce, has been noted in this application. The term should be accompanied by the generic terminology; furthermore the term should be capitalized wherever it appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
Appropriate correction is required.
The abstract of the disclosure is objected to because the abstract mixes the terms aminotransferase and transaminase. One term should be used consistently. A corrected abstract of the disclosure is required and must be presented on a separate sheet, apart from any other text. See MPEP § 608.01(b).
Claim Rejections - 35 USC § 112
Claims 1, 2, 5 and 6 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.
Regarding claims 1 and 2, “When a subjective term is used in the claim, the examiner should determine whether the specification supplies some objective standard for measuring the scope of the term. Some objective standard must be provided in order to allow the public to determine the scope of the claim. A claim term that requires the exercise of subjective judgment without restriction may render the claim indefinite.” MPEP 2173.05(IV). Claim 1 recites “with broad substrate spectrum.” What range of substrate utilization may or may not constitute “broad substrate spectrum” is a subjective determination in the absence of any objective standard for the same in the art or the specification. Since there is no objective standard for “with broad substrate spectrum” in the art or in the specification, an exercise of subjective judgment without restriction is required to differentiate between:
A P. putida omega-transaminase having broad substrate spectrum as encoded by a nucleotide sequence of SEQ ID NO: 1 or having an amino acid sequence of SEQ ID NO: 2 as to be an embodiment of the claims; and
A P. putida omega-transaminase not having broad substrate spectrum as encoded by a nucleotide sequence of SEQ ID NO: 1 or having an amino acid sequence of SEQ ID NO: 2 as not to be an embodiment of the claims.
For this reason, an ordinarily skilled artisan cannot determine how to avoid infringement of claims 1 and 2.
Claim 5 contains the trademark/trade name pCold I and pCold II. Where a trademark or trade name is used in a claim as a limitation to identify or describe a particular material or product, the claim does not comply with the requirements of 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph. See Ex parte Simpson, 218 USPQ 1020 (Bd. App. 1982). The claim scope is uncertain since the trademark or trade name cannot be used properly to identify any particular material or product. A trademark or trade name is used to identify a source of goods, and not the goods themselves. Thus, a trademark or trade name does not identify or describe the goods associated with the trademark or trade name. In the present case, the trademark/trade name is used to identify/describe a material and, accordingly, the identification/description is indefinite. The mark pCold™ is asserted as a trademark by Taka Bio Inc. as indicated at the following web address: https://www.takarabio.com/about/trademarks.
Claim 6 contains the trademark/trade name BL21 Star(DE3), Origami series and Shuffle T7. Where a trademark or trade name is used in a claim as a limitation to identify or describe a particular material or product, the claim does not comply with the requirements of 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph. See Ex parte Simpson, 218 USPQ 1020 (Bd. App. 1982). The claim scope is uncertain since the trademark or trade name cannot be used properly to identify any particular material or product. A trademark or trade name is used to identify a source of goods, and not the goods themselves. Thus, a trademark or trade name does not identify or describe the goods associated with the trademark or trade name. In the present case, the trademark/trade name is used to identify/describe a product and, accordingly, the identification/description is indefinite. SHuffle® is a registered trademark 5719636. Origami™ is an asserted trademark of Novagen. BL21 Star(DE3)™is an asserted trademark of ThermoFisher Scientific. See www.thermofisher.com/us/en/home/global/trademark-information.html
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 1-6 (all pending claims) rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
The purpose of the written description requirement is to ensure that the inventor had possession, at the time the invention was made, of the specific subject matter claimed. For a broad generic claim, the specification must provide adequate written description to identify the genus of the claim.
“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." Fiers, 984 F.2d at 1171, 25 USPQ2d 1601; In re Smythe, 480 F.2d 1376, 1383, 178 USPQ 279, 284985 (CCPA 1973) (“In other cases, particularly but not necessarily, chemical cases, where there is unpredictability in performance of certain species or subcombinations other than those specifically enumerated, one skilled in the art may be found not to have been placed in possession of a genus.”). Regents of the University of California v. Eli Lilly & Co., 119, F.3d 1559, 1568, 43 USPQ2d 1398, 1405 (Fed. Cir. 1997).
“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 the applicant was in possession of the claimed genus.” MPEP 2163(II)(3)(a).
Furthermore, 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 disclosure of only one species encompassed within a genus adequately describes a claim directed to that genus only if the disclosure ‘indicates that the patentee has invented species sufficient to constitute the gen[us].’ See Enzo Biochem, 323 F.3d at 966, 63 USPQ2d at 1615; Noelle v. Lederman, 355 F.3d 1343, 1350, 69 USPQ2d 1508, 1514 (Fed. Cir. 2004) (Fed. Cir. 2004) (‘[A] patentee of a biotechnological invention cannot necessarily claim a genus after only describing a limited number of species because there may be unpredictability in the results obtained from species other than those specifically enumerated.’). ‘A patentee will not be deemed to have invented species sufficient to constitute the genus by virtue of having disclosed a single species when … the evidence indicates ordinary artisans could not predict the operability in the invention of any species other than the one disclosed.’ In re Curtis, 354 F.3d 1347, 1358, 69 USPQ2d 1274, 1282 (Fed. Cir. 2004).” MPEP 2163(II)(3)(a).
Claims 1 and 4 recites an omega-transaminase gene “comprising a nucleotide sequence shown in SEQ ID NO: 1” and claims 2 and 3 recites an omega-transaminase “comprising an amino acid sequence shown in SEQ ID NO: 2.” The recitation of indefinite articles a/an indicates a genus of plural sequences such that reference to “a nucleotide sequence” as shown in SEQ ID NO: 1 refers to any fragment of SEQ ID NO: 1 including as few as two consecutive nucleotides and “an amino acid sequence” as shown in SEQ ID NO: 2 refers to any fragment of SEQ ID NO: 2 including as few as two consecutive amino acid residues. It is further noted that the recited transaminase-encoding gene in claim 1 is required to be a Pseudomonas putida omega-transaminase with broad substrate spectrum that extends to the same as being requirements of the encoded omega-transaminase as well as recited in claim 2. Claims 3 and 4 further requires a Pseudomonas putida omega-transaminase but do not require broad substrate spectrum.
As such, claims 1-3 (and claims depending therefrom) encompass a genus of omega-transaminases defined as requiring only a few (and as few as two) amino acids as found in SEQ ID NO: 2 or encoded by SEQ ID NO: 1. “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,” and a “‘representative number of species’ means that the species which are adequately described are representative of the entire genus.” While the claims further require a Pseudomonas putida omega-transaminase, what structure separates a Pseudomonas putida omega-transaminase from other omega-transaminases, wherein 100% identity to SEQ ID NO: 2, is not required is not clear. The specification discloses a species of omega-transaminase that is 100% identical to the full-length sequence of SEQ ID NO: 2 as also encoded by SEQ ID NO: 1. The specification has no description that can allow for an ordinarily skilled artisan at the time of filing to make a reasonable identification of member species of the discussed species of omega-transaminases requiring only a few (and as few as two) amino acid residues of SEQ ID NO: 2 as can be encoded by a sequence as shown in SEQ ID NO: 1, and due to the large number of potential transaminase species falling within the discussed genus of transaminases the description of a transaminases identical to the full-length of SEQ ID NO: 2 cannot be considered to be a “representative” number of species that adequately describes the entire genus discussed, particularly wherein such genes requires the encompassed transaminases further to have a broad substrate spectrum. That is, the recited genus of transaminases includes species having very low sequence identity to SEQ ID NO: 2 (e.g. less than 30%, less than 20%, less than 10% identity) wherein members of the recited genus cannot be reasonably identify based off of the disclosure of only one full-length sequence of SEQ ID NO: 2 wherein species that are members of the discussed genus include those that are 1) wild-type or transaminase sequences otherwise known in the art, and 2) are non-naturally occurring or variant transaminases sequences requiring no significant sequence identity to any known omega-transaminase sequence. “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." Here, when presented with any potential amino acid sequence of a transaminases sequence with little (e.g. less than 30%, less than 20%, less than 10% identity) to SEQ ID NO: 2 it is not reasonable possible to determine if the same 1) has activity as an omega-transaminase with broad substrate specificity as to be a member of the discussed genus, or 2) lacks such activity as to not be a member of the discussed genus. For these reasons, the as-filed specification lacks a sufficient written description of the genus of transaminases and encoded genes recited in claims 1 and 2.
This rejection may be obviated by amending the claims to recite “has the amino acid sequence as shown in SEQ ID NO: 2” and “the nucleotide sequence as shown in SEQ ID NO: 1.”
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) 1-6 (all pending claims) is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Zhang et al. (A high-throughput microtiter plate assay for the discovery of active and enantioselective amino alcohol-specific transaminases, Analytical Biochem. 518, 2017, 94-101) as evidenced by Shin et al. (Structural dynamics of the transaminase active site revealed by the crystal structure of a cofactor free omega-transaminase from Vibrio fluvialis JS17, Sci. Reports 8, 2018, 11454).
The rejections under 35 U.S.C. 112(a) above including interpretation of the broadest reasonable scope of claims 1 and 2 set forth above are incorporated herein by reference.
Abstract:
Chiral vicinal amino alcohols are important chiral building blocks and intermediates in the pharmaceutical industry. The transaminase (TAm) catalyzed kinetic resolution of racemic amino alcohols provides a straightforward approach to access these important compounds. This study describes the development of a novel microtiter plate assay to screen vicinal amino alcohol-specific TAms using a tetrazolium red-based colorimetric assay to monitor the rate of α-hydroxy ketone formation at 510 nm. This approach is the first to determine the Michaelis-Menten parameters for a recombinant TAm (PpbauA) from Pseudomonas putida NBRC14164. The corresponding Vmax and KM values for both enantiomers of 2-amino-1-propanol and 2-amino-1-butanol were obtained, and the calculated kinetic E-factors of PpbauA toward 2-amino-1-propanol and 2-amino-1-butanol are 3 (S) and 6 (R), respectively. The method is sensitive and exhibits low level background coloration. Moreover, this method can be used to detect transaminase activity and enantioselectivity toward amino alcohols in a high-throughput format. Additionally, this simple method is compatible with the most widely used (R)- and (S)-selective transaminases and may be a broadly applicable tool for screening transaminases from a transaminase mutant library.
“For cloning of PpTAs (Pp21050, Pp36420, PpspuC and PpbauA) from Pseudomonas putida NBRC14164, genomic DNA from Pseudomonas putida NBRC14164 was used as the PCR template. The transaminase genes were amplified by PCR.” Zhang, Sec. 2.3. “The PCR product was isolated and digested with the BamHI and XhoI restriction endonucleases and cloned into the pET28a (+) vector. E. coli BL21 (DE3) competent cells were transformed with the recombinant plasmids to yield E. coli (Pp21050), E. coli (PpbauA), E. coli (Pp36420) and E. coli (PpspuC).” Zhang, sec. 2.3.
“The verified clone was grown in the terrific broth (TB) medium, which contained 50 μg mL−1 kanamycin at 37 °C. The culture was grown until an OD600 of 0.6 was achieved, and it was treated with 0.5 mM IPTG (final concentration). The growth of the culture was maintained at 20 °C with vigorous shaking for 12 h. Cells were harvested by centrifugation at 8000 g for 10 min at 4 °C, washed twice with sodium phosphate buffer (100 mM, pH 8.0) and resuspended in the same buffer. To disrupt the cells [i.e. lyse], the cell suspension (10 g cdw L−1) was placed on ice and sonicated for 10 min at 400 W for 4 s at 4 s intervals. After centrifugation, the cell lysate supernatants [i.e. crude enzyme solution] were stored at −20 °C for further use.” Zhang, sec. 2.4.
The above is a description of a method of preparing an enzyme preparation with the described PpspuC transaminase by expressing a Pseudomonase putida omega-transaminase in an e. coli BL21 (DE3) host cell [from a pET-28a vector] to obtain a recombinant cell; lysing the recombinant cell to obtain crude enzyme solution.
Table 2 and Fig. 3 of Zhang shows the PpspuC transaminase from P. putida has activity with at least 5 different amine donors including (R)-1a, (S)-1a, (R)-1b, (S)-1b and (R)-1d, which is within the broadest reasonable interpretation of “broad substrate spectrum.” An omega-transferase is considered to be an enzyme that is capable of using an amine donor having no carboxylic acid group, wherein amine donors (R)-1a, (S)-1a, (R)-1b, (S)-1b and (R)-1d do not have carboxylic acid groups such that the PpspuC transaminase from P. putida is an omega-transaminase. See Shin, abstract, as evidence for definition of an omega-transaminase as understood in the prior art: Omega (ω)-transaminase catalyzes the transfer of an amino group from a non-α position amino acid, or an amine compound with no carboxylic group, to an amino acceptor.
The gene sequence encoding PpspuC from Zhang is provided in the Supplemental Material of Zhang where an alignment with recited SEQ ID NO: 1 and an alignment of the amino acid translation thereof with recited SEQ ID NO: 2 are as follows:
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Due to the substantial identity between the PpspuC transaminase gene from P. putida reported by Zhang and recited SEQ ID NO: 1, the same comprises a nucleotide sequence shown in SEQ ID NO: 1. Similarly, due to the similarity between the amino acid sequence encoded by the PpspuC transaminase from P. putida reported by Zhang and recited SEQ ID NO: 2, the same comprises an amino acid sequence shown in SEQ ID NO: 2. Further, the procedures described in sections 2.3 and 2.4 of Zhang excerpted above meet the features of claims 4-6.
This rejection may be overcome by amending the claims to require the entire sequence of SEQ ID NO: 1 or 2.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1 and 2 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a natural phenomenon without significantly more. The claim(s) recite(s) a P. putida omega-transaminase . This judicial exception is not integrated into a practical application because the claims do not recite any limitations that can be deemed to be a practical elements. The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the claims do not recite additional elements.
MPEP 2106(III) directs that claims drawn to 1) a composition of matter (step 1), 2) a law of nature or a natural phenomenon or a product of nature (step 2A) and 3) lacking recitation of additional elements that make the claims directed to significantly more than a judicial exception (step 2B) are ineligible for patenting under 35 U.S.C. 101. See MPEP 2106(III), flow chart. Step 2A into two prongs as set forth in MPEP 2106.04(II)(A).
“If the claim includes a nature-based product that does not exhibit markedly different characteristics from its naturally occurring counterpart in its natural state, then the claim recites a "product of nature" exception, and requires further analysis in Step 2A Prong Two to determine whether the claim as a whole integrates the exception into a practical application.” MPEP 2106.04(c). “It is important to keep in mind that product of nature exceptions include both naturally occurring products and non-naturally occurring products that lack markedly different characteristics from any naturally occurring counterpart.” MPEP 2106.04(b)(II).
“The markedly different characteristics analysis is part of Step 2A Prong One, because the courts use this analysis to identify product of nature exceptions.” MPEP 2106.04(c). “The markedly different characteristics analysis compares the nature-based product limitation to its naturally occurring counterpart in its natural state. Markedly different characteristics can be expressed as the product’s structure, function, and/or other properties, and are evaluated based on what is recited in the claim on a case-by-case basis. If the analysis indicates that a nature-based product limitation does not exhibit markedly different characteristics, then that limitation is a product of nature exception. If the analysis indicates that a nature-based product limitation does have markedly different characteristics, then that limitation is not a product of nature exception.” MPEP 2106.04(c)(II).
Examiners should keep in mind that if the nature-based product limitation is naturally occurring, there is no need to perform the markedly different characteristics analysis because the limitation is by definition directed to a naturally occurring product and thus falls under the product of nature exception.” MPEP 2106.04(c)(I).
The rejected claims recite a product such that step 1 is met with respect to the judicial exception.
The rejections under 35 U.S.C. 102(a)(1) set forth above are incorporated herein by reference. The PpspuC gene from Pseudomonas putida NBRC14164 is understood to be a naturally-occurring gene from a naturally-occurring microorganism as to a nature-based product. See Ohji et al. (The Complete Genome Sequence of Pseudomonas putida NBRC 14164T Confirms High Intraspecies Variation, Genome Announcements, 2, 2014, e00029-14), cited by Zhang (reference 41), as source of Pseudomonas putida NBRC14164 genome, where the same is understood to be a natural-occurring microorganism. As such, the encoded omega-transaminase is also a nature-based product. As discussed above, such a gene and encoded omega-transaminase meets the features of claims 1 and 2.There is no need to perform the markedly different characteristics analysis because the limitations with respect to the recited gene and omega-transaminase is by definition directed to a naturally occurring product and thus falls under the product of nature exception such that step 2A, prong one, is met for establishing a judicial exception.
For step 2A, prong two, “Prong Two asks does the claim recite additional elements that integrate the judicial exception into a practical application? In Prong Two, examiners evaluate whether the claim as a whole integrates the exception into a practical application of that exception.” MPEP 2106(II)(A)(2). For step 2B, Step 2B asks: Does the claim recite additional elements that amount to significantly more than the judicial exception”? MPEP 2106.05(II). Here, the claims do not recite any additional elements other than the natural-product omega-transferase and its encoding gene as discussed above. As such, Step 2A, prong two, and step 2B are answered in favor of establishing a judicial exception.
The claims are directed towards ineligible subject matter for the reasons stated.
It is noted that is the claims were amended to recite a gene having 100% identity to SEQ ID NO: 1 and a transaminase having 100% identity to SEQ ID NO: 2, the analysis above would apply to such amended claims if the novel Pseudomonas putida referenced in para. [0036] of the specification is also a product of nature. The preceding is an observation and not a basis for the present rejection of claims 1 and 2 under 35 U.S.C. 101.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to TODD M EPSTEIN whose telephone number is (571)272-5141. The examiner can normally be reached Mon-Fri 9:00a-5:30p.
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/TODD M EPSTEIN/Primary Examiner, Art Unit 1652
/ROBERT B MONDESI/Supervisory Patent Examiner, Art Unit 1652
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