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 .
Priority
This application claims benefit of priority to Foreign Application No. CN 202111170973.6 filed 10/08/2021 and is also a 371 of PCT/CN2021/135645 filed 12/06/2021. Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55. However, an English translation of the foreign patent document was not provided. Therefore, for the purposes of applying prior art, the effective filing date of the claimed invention is the filing date of the PCT, 12/06/2021.
Information Disclosure Statement
The Information Disclosure Statement filed 04/05/2024 has been acknowledged and considered.
Drawings
The Drawings filed 04/05/2024 are accepted by the Examiner.
Amendments and Claim Status
In the preliminary amendment filed 04/05/2024, Applicant canceled claims 18-28 and added new claims 29-31.
Claims 1-17 and 29-31 are currently pending and under examination.
Claim Objections
Claims 3-4, 6 and 8 are objected to because of the following informalities: Claims 3-4, 6 and 8 recite “a sequence of the … is as shown in SEQ ID NO.” While the phrase “a sequence of the … is as shown in SEQ ID NO.” is interpreted to mean any sequence within the specific SEQ ID NO., this limitation would be better stated as “the sequence of the … is SEQ ID NO.” Appropriate correction is required.
Claim Rejections - 35 USC § 112
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.
Claim 17 is rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the enablement requirement. The claim contains subject matter which was not described in the specification in such a way as to enable one skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention.
The invention appears to employ novel biological materials, specifically Bacillus licheniformis BN11 deposited in the China Center for Type Culture Collection on 01/08/2016 as CCTCC NO: M2016026. Since the biological materials are essential to the claimed invention they must be obtainable by a repeatable method set forth in the specification or otherwise readily available to the public. If the biological materials are not so obtainable or available, the requirements of 35 U.S.C. § 112 may be satisfied by a deposit of the biological materials. It appears this deposit was not made under the Budapest Treaty. Additionally, Applicant has not provided an assurance statement.
If the deposit is made under the Budapest Treaty, then an affidavit or declaration by Applicant, or a statement by an attorney of record over his or her signature and registration number, stating that the specific biological materials have been deposited under the Budapest Treaty and that the biological materials will be irrevocably and without restriction or condition released to the public upon the issuance of a patent, would satisfy the deposit requirement made herein. If the deposit has not been made under the Budapest Treaty, then in order to certify that the deposit meets the criteria set forth in 37 C.F.R. §§ 1.801-1.809, Applicant may provide assurance of compliance by an affidavit or declaration, or by a statement by an attorney of record over his or her signature and registration number, showing that:
(a) during the pendency of this application, access to the invention will be afforded to
the Commissioner upon request;
(b) all restrictions upon availability to the public will be irrevocably removed upon
granting of the patent;
(c) the deposit will be maintained in a public depository for a period of 30 years or 5
years after the last request or for the effective life of the patent, whichever is longer;
(d) a test of the viability of the biological material at the time of deposit will be made
(see 37 C.F.R. § 1.807); and
(e) the deposit will be replaced if it should ever become inviable.
Applicant's attention is directed to M.P.E.P. §2400 in general, and specifically to §2411.05, as well as to 37 C.F.R. § 1.809(d), wherein it is set forth that "the specification shall contain the accession number for the deposit, the date of the deposit, the name and address of the depository, and a description of the deposited material sufficient to specifically identify it and to permit examination." The specification should be amended to include this information, however, Applicant is cautioned to avoid the entry of new matter into the specification by adding any other information.
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 3, 6,, 11 and 16 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claims 3 and 11 recite “a D-lactate dehydrogenase gene ldhTi”. It appears ldhTi is a specific D-lactate dehydrogenase gene because D-lactate dehydrogenase genes are generally referred to as ldhA or ldhD, however, one of ordinary skill in the art would not be reasonably apprised of which specific D-lactate dehydrogenase gene ldhTi is as it is not a well-known gene nor does the instant Specification delineate which D-lactate dehydrogenase gene ldhTi is. Thus, claims 3 and 11, and all claims dependent upon claims 3 and 11, are indefinite. For the purposes of compact prosecution, ldhTi is being interpreted as any D-lactate dehydrogenase gene.
Regarding claims 3 and 6, the term “preferably” renders the claim indefinite because it is unclear whether the limitations following the phrase are part of the claimed invention. See MPEP § 2173.05(d).
Claim 6 recites “wherein the promoter is Pals” in line 1 of the claim. It appears Pals is a specific promoter, however, one of ordinary skill in the art would not be reasonably apprised of which specific promoter Pals is as it is not a well-known promoter nor does the instant Specification delineate what a Pals promoter is. Thus, claim 6 is indefinite.
Regarding claim 16, the phrase “or a derivative thereof” renders the claim indefinite because the claim includes elements not actually disclosed (those encompassed by “or a derivative thereof”), thereby rendering the scope of the claim unascertainable. See MPEP § 2173.05(d). Additionally, it is noted the instant Specification does not define what a ‘derivative’ is, only provides two examples of what the derivative could be while also indicating the derivative is “not limited to” to the two examples given (Specification, Page 27, Paragraph 4). It is unclear if the derivative has to be a species of B. licheniformis, if it can be any species within the genus of Bacillus or if the derivative can be any bacteria that possesses a pyruvate synthesis pathway since this is the only required function of the original strain. It is unclear how far the ‘derivative’ can deviate and still be considered a derivative. Thus, the scope of the claim is unascertainable because the boundaries of the protected subject matter are not clearly delineated, leaving the metes and bounds of ‘or a derivative thereof’ unclear, rendering claim 16 indefinite.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1-3, 5-12 and 29 are rejected under 35 U.S.C. 103 as being unpatentable over Zhang et al. (US 20150247174 A1, 09/03/2015) (IDS Reference of 04/05/2024) in view of Yamamoto et al. (Applied and Environmental Microbiology, 2012) (IDS Reference of 04/05/2024) as evidenced by Francis et al. (Current Protocols in Protein Science, 2010).
Regarding claims 1-2 and 9-10, Zhang et al. disclose the purpose of the invention is to provide a DL-alanine producing engineered bacterium wherein the engineered bacterium can directly produce DL-alanine using glucose with a high yield and a short production cycle (Paragraph [0004]). Further, to create the engineered bacterium, the lactate dehydrogenase gene, pyruvate formate lyase gene, alcohol dehydrogenase gene and methylglyoxal synthase gene are inactivated on the original chromosome and an exogenous L-alanine dehydrogenase gene and an exogenous alanine racemase gene are integrated into the original chromosome (Paragraph [0005]). The exogenous L-alanine dehydrogenase gene was derived from Geobacillus stearothermophilus, reading on a GSald gene, and the exogenous alanine racemase gene was derived from Bacillus subtilis (Paragraph [0007]). Regarding the GSald gene being thermostable at 42°C to 55°C, Zhang et al. disclose fermenting the engineered bacterium at 42°C, therefore, it would be expected the GSald gene would be thermostable at 42°C. Additionally, Escherichia coli is the construction bacterium, reading on original strain possessing a pyruvate synthesis pathway (See Figure 1 of Zhang et al.), of the DL-alanine producing engineered bacterium (Paragraph [0006]).
Zhang et al. do not disclose a step of inserting a 6-phosphofructokinase gene pfk or a pyruvate kinase gene pyk into the engineered bacterium.
However, Yamamoto et al. disclose the overexpression of genes encoding glycolytic enzymes enhances glucose metabolism and alanine production (Title). More specifically, Yamamoto et al. disclose chromosomal integration of pyruvate kinase-encoding pyk and phosphofructokinase-encoding pfk into a strain, creating a recombinant strain called GLY2 (Abstract). Strain GLY2 improved the rate of alanine formation by 20% compared to a strain without the pyk and pfk genes (Abstract).
Thus, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have inserted a copy of a pfk gene and a pyk gene into the engineered bacterium of Zhang et al. motivated by the desire to create a bacterium that can effectively produce alanine because the engineered bacterium of Zhang et al. is directed to increasing the yield of DL-alanine and Yamamoto et al. teach the introduction of a pfk gene and a pyk gene improves the yield of alanine when introduced into a recombinant microorganism.
Regarding claim 3, see 112b above. As discussed above, Zhang et al. disclose inactivating the lactate dehydrogenase gene in the original strain (Paragraph [0005]). Zhang et al. further depict the pathway from glucose to DL-alanine in Figure 1, including the inactivated and introduced genes (Paragraph [0012] and Fig 1 of Zhang et al.). Figure 1 specifically shows the inactivation of lactate dehydrogenase prevents the formation of D-lactic acid. Thus, it appears, absent evidence to the contrary, the inactivated lactate dehydrogenase gene is a D-lactate dehydrogenase gene.
Zhang et al. do not disclose the original strain possesses a lactate dehydrogenase gene and a D-lactate dehydrogenase gene or inactivating or deleting both genes.
However, Zhang et al. disclose the specific genes that are inactivated in the engineered bacterium are inactivated to avoid synthesizing byproducts, such as lactic acid, such that the raw material saccharides metabolized according to the defined pathways synthesize specifically DL-alanine (Paragraph [0012]).
Thus, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have deleted all lactate dehydrogenase genes present in the original strain, including lactate dehydrogenase and D-lactate dehydrogenase, to minimize the formation of byproducts, such as lactic acid, as taught by Zhang et al. motivated by the desire to promote the formation of the desired product, DL-alanine.
Regarding claim 5, as discussed above, Zhang et al. disclose an exogenous L-alanine dehydrogenase gene and an exogenous alanine racemase gene are integrated into the original chromosome (Paragraph [0005]). Zhang et al. further disclose the DL-alanine producing engineered bacterium was constructed by a trc promoter upstream of the inserted gene (Paragraph [0010]).
Regarding claim 6, see 112b above. As it is unclear exactly what a Pals promoter is, the trc promoter disclosed by Zhang et al. reads on a Pals promoter.
Regarding claim 7, as discussed above, Zhang et al. disclose the use of the trc promoter (Paragraph [0010]), reading on a strong promoter as evidenced by Francis et al., and an exogenous alanine racemase gene was derived from Bacillus subtilis (Paragraph [0006]), reading on the inserted alanine racemase gene alr1 or alr2. Francis et al. disclose trc is considered to be a strong promoter (Page 10, Right Column, Paragraph 2).
Regarding claim 8, Zhang et al. disclose the exogenous racemase gene has a sequence as set forth by SEQ ID NO: 14 (Paragraph [0009]). SEQ ID NO: 14 of Zhang et al. shares 44.1% sequence identity and 66.1% local similarity to instant SEQ ID NO: 2, reading on a sequence of the alanine racemase gene alr1 as shown in SEQ ID NO: 2. It is noted ‘a sequence of’ is broad enough to read on any sequence of nucleic acids in SEQ ID NO: 2. A sequence alignment is provided below wherein Qy is SEQ ID NO: 14 of Zhang et al. and Db is instant SEQ ID NO: 2.
PNG
media_image1.png
864
638
media_image1.png
Greyscale
PNG
media_image2.png
650
658
media_image2.png
Greyscale
Regarding claim 11, see 112b above. As discussed above, Zhang et al. disclose the purpose of the invention is to provide a DL-alanine producing engineered bacterium wherein the engineered bacterium can directly produce DL-alanine using glucose with a high yield and a short production cycle (Paragraph [0004]). Further, to create the engineered bacterium, the lactate dehydrogenase gene, pyruvate formate lyase gene, alcohol dehydrogenase gene and methylglyoxal synthase gene are inactivated on the original chromosome and an exogenous L-alanine dehydrogenase gene and an exogenous alanine racemase gene are integrated into the original chromosome (Paragraph [0005]). Zhang et al. depict the pathway from glucose to DL-alanine in Figure 1, including the inactivated and introduced genes (Paragraph [0012] and Fig 1 of Zhang et al.). Figure 1 specifically shows the inactivation of lactate dehydrogenase prevents the formation of D-lactic acid. Thus, it appears, absent evidence to the contrary, the inactivated lactate dehydrogenase gene is a D-lactate dehydrogenase gene. Also, the exogenous L-alanine dehydrogenase gene was derived from Geobacillus stearothermophilus, reading on a GSald gene, and the exogenous alanine racemase gene was derived from Bacillus subtilis (Paragraph [0007]). Additionally, Escherichia coli is the construction bacterium, reading on original strain, of the DL-alanine producing engineered bacterium (Paragraph [0006]). It is noted the instant Specification states overexpressing an alanine racemase gene can be achieved by insertion of a strong promoter (Specification, Page 23, Last Sentence – Page 24, First Sentence). Zhang et al. disclose the use of a trc promoter for expressing the alanine racemase gene (Paragraph [0010]). The trc promoter is a strong promoter as evidenced by Francis et al. Francis et al. disclose trc is considered to be a strong promoter (Page 10, Right Column, Paragraph 2). Thus, the disclosure of Zhang et al. of the alanine racemase gene being under the control of a trc promoter reads on an overexpression of an alanine racemase gene alr1 or alr2.
Zhang et al. go on to state by integrating the exogenous alanine racemase gene into the engineered bacterium, partial L-alanine was converted into D-alanine, achieving the direct product of DL-alanine from raw material saccharides, thereby decreasing the production cycle of DL-alanine (Paragraph [0012]). Additionally, the introduction of the exogenous alanine racemase gene enabled half of the L-alanine as produced to be converted into D-alanine so that the optical purity ratio between L-alanine and D-alanine was 50:50 (Paragraph [0012]).
Zhang et al. do not disclose a step of inserting a 6-phosphofructokinase gene pfk or a pyruvate kinase gene pyk into the engineered bacterium, or knocking out an alr1 and an alr2 gene.
However, Yamamoto et al. disclose the overexpression of genes encoding glycolytic enzymes enhances glucose metabolism and alanine production (Title). More specifically, Yamamoto et al. disclose chromosomal integration of pyruvate kinase-encoding pyk and phosphofructokinase-encoding pfk into a strain, creating a recombinant strain called GLY2 (Abstract). Strain GLY2 improved the rate of alanine formation by 20% compared to a strain without the pyk and pfk genes (Abstract).
Thus, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have inserted a copy of a pfk gene and a pyk gene into the engineered bacterium of Zhang et al. motivated by the desire to create a bacterium that can effectively produce alanine because the engineered bacterium of Zhang et al. is directed to increasing the yield of DL-alanine and Yamamoto et al. teach the introduction of a pfk gene and a pyk gene improves the yield of alanine when introduced into a recombinant microorganism.
It would have been further obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have knocked out all alanine racemase genes, including alr1 and alr2, in the original strain because the introduced exogenous alanine racemase gene enables half of the produced L-alanine to be converted into D-alanine as taught by Zhang et al. motivated by the desire to create a product with 50% D-alanine and 50% L-alanine, being DL-alanine.
Regarding claims 12 and 29, Zhang et al. disclose the fermentation temperature was 42°C (Paragraph [0057]). Thus, it would be expected, absent evidence to the contrary, that the original strain would be capable of producing DL-alanine at 42°C.
Claims 1-17 and 29-31 are rejected under 35 U.S.C. 103 as being unpatentable over Zhang et al. (US 20150247174 A1, 09/03/2015) (IDS Reference of 04/05/2024) in view of Yamamoto et al. (Applied and Environmental Microbiology, 2012) (IDS Reference of 04/05/2024) as evidenced by Francis et al. (Current Protocols in Protein Science, 2010) and further in view of Jaitzig et al. (US 10837034 B2, 11/17/2020) as evidenced by Zalma et al. (Science Progress, 2021).
Regarding claim 4, neither Zhang et al. nor Yamamoto et al. disclose the alanine dehydrogenase gene comprises a sequence as shown in SEQ ID NO: 1.
However, Jaitzig et al. disclose a recombinant microorganism for the fermentative production of alanine (See entire document, Abstract). More specifically, a process for the fermentative production of alanine (Column 25, Lines 27-39) wherein the recombinant microorganism has an introduced, increased or enhanced activity and/or expression of an alaD gene encoding an alanine dehydrogenase (Column 6, Lines 1-24). Jaitzig et al. further disclose the alaD gene is from Geobacillus stearothermophilus (Column 6, Line 35), reading on a GSald gene, wherein the alaD gene comprises the nucleic acid sequence of SEQ ID NO: 1 or a sequence with at least 80% sequence identity to SEQ ID NO:1 (Column 10, Lines 31-40). SEQ ID NO:1 of Jaitzig et al. shares 72.1% sequence identity and 82.6% local similarity to instant SEQ ID NO:1., reading on a sequence of the gene for alanine dehydrogenase as shown in SEQ ID NO:1. A sequence alignment is provided below wherein Qy represents instant SEQ ID NO:1 and Db represents SEQ ID NO:1 disclosed by Jaitzig et al.
PNG
media_image3.png
832
624
media_image3.png
Greyscale
PNG
media_image4.png
836
642
media_image4.png
Greyscale
Thus, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have utilized the alaD gene disclosed by Jaitzig et al. in the method of Zhang et al. motivated by the desire to engineer a bacterium that can effectively produce alanine because the alaD gene of Jaitzig et al. was a known and effective alanine dehydrogenase from Geobacillus stearothermophilus utilized in a recombinant microorganism for producing alanine as taught by Jaitzig et al. and Zhang et al. specifically state their alanine dehydrogenase is from Geobacillus stearothermophilus and is for producing alanine.
Regarding claims 13-15 and 30-31, Zhang et al. disclose since a bacterium experiences L-alanine metabolism, the solution as defined above, being the construction of the engineered bacterium, can be achieved in all conventional bacteria.
Neither Zhang et al. nor Yamamoto et al. disclose the original strain is a thermophilic strain, Bacillus, or more specifically, B. lichenformis, B. coagulans, B. methylotrophicus, B. inulinus, or Geobacillus stearothermophilus.
However, Jaitzig et al. disclose species of the genus Bacillus can be utilized, including B. subtilis, B. lichenformis and B. amyloliquefaciens (Column 4, Lines 25-30). B. subtilis, B. lichenformis and B. amyloliquefaciens are all thermophilic strains, as evidenced by Zalma et al. Zalma et al. disclose multiple species of Bacillus that are thermophilic strains, including B. subtilis, B. lichenformis and B. amyloliquefaciens (Table 1 of Zalma et al.).
Thus, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have utilized any of B. subtilis, B. lichenformis and B. amyloliquefaciens as the original strain in the engineered bacterium of Zhang et al. motivated by the desire to create a bacterium capable of producing DL-alanine because Zhang et al. specifically state all conventional bacteria can be utilized in their method and Jaitzig et al. teach B. subtilis, B. lichenformis and B. amyloliquefaciens are all usable original strains for producing alanine.
Regarding claim 16, see 112b above. As discussed immediately above, Jaitzig et al. disclose the utilized bacterial strain is B. lichenformis. As it is unclear exactly what ‘a derivative’ is, the disclosure of Jaitzig et al. of B. lichenformis reads on a derivative of B. lichenformis ATCC 14580.
Regarding claim 17, it is noted the only identifying information given by the instant Specification about B. lichenformis BN11 deposited as CCTCC NO: M2016026 is that it is a lactate-producing strain constructed from ATCC 14580 (Specification, Page 35, Paragraph 5). It is further noted a deposit number is simply an identifier, it does not distinguish the deposited strain from any other B. lichenformis strain absent a sequence or other definable characteristics. Thus, the B. lichenformis disclosed by Jaitzig et al. reads on B. lichenformis BN11 as Jaitzig et al. disclose a product of fermentation is lactate (Column 25, Lines 27-39) and the only characteristic given of B. lichenformis BN11 is that it can produce lactate.
Conclusion
Claims 1-17 and 29-31 are rejected.
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to ASHLEY T WHITE whose telephone number is (571)272-0683. The examiner can normally be reached Monday - Friday 8:30 - 5:00 EST.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Sharmila Landau can be reached at (571)272-0614. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/A.T.W./Examiner, Art Unit 1653
/SHARMILA G LANDAU/Supervisory Patent Examiner, Art Unit 1653
Prosecution Insights