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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on July 28, 2025 has been entered.
DETAILED ACTION
The instant application is a U.S. national phase of PCT/EP2020/055299, filed February 28, 2020 with foreign priority EP19160379.4, filed March 1, 2019.
Applicant’s amendment filed July 28, 2025 is acknowledged. Claims 15-16 and 19-20 are canceled, and claim 24 is newly added. Claims 13-14 and 22 are amended. Currently claims 1-14, 17-18, and 21-24 are pending; and claims 1-12 are withdrawn.
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 13, 14, 17, 18, 21-22, and 24 are rejected under 35 U.S.C. 103 as being unpatentable over Maertens et al. (WO 2012/007481 A2, cited in PTO-892 mailed 8/2/2024, hereinafter “Maertens”) in view of Chandran et al. (Biotechnol. Prog. 2003, 19, 808-814, hereinafter “Chandran”), Weisser et al. (JOURNAL OF BACTERIOLOGY, June 1995, p. 3351–3354, hereinafter “Weisser”), and Lendenmann et al. (APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 1996, Vol. 62: 5, 1493–1499, cited in PTO-892 mailed 8/2/2024, hereinafter “Lendenmann”).
Maertens teaches genetically engineered organisms for the production of bio-products, such as specialty saccharides, inter alia, in fermentative processes (abstract). Maertens teaches the engineered microorganisms produce a desired product, such as carbohydrate, by reducing or eliminating the activity of enzymes catalyzing reactions converting metabolites from the 'biomass and/or bio-catalytic enzyme and/or cofactor supplementation part' into metabolites from the 'production pathway' part and vice versa, e.g. by reducing or eliminating/knocking-out at least one, some or all the genes encoding for enzymes performing reactions which convert the production pathway intermediates into biomass precursors (pg. 6, lines 8-13). For example, Maertens teaches a mutant strain comprises the main reactions able to convert a glucose-1-phosphate to biomass production were eliminated, and thus the glucose-1-phosphate accumulated intracellularly, which meets the limitation in claim 13 (pg. 33, Example 4). Maertens teaches such carbohydrate products are 1,2-fucosyllactose, 1,3-fucosyl lactose, 1,4-fucosyllactose, inter alia, which meets the limitation of claim 14 (pg. 9, lines 10-15). Maertens teaches a microorganism that is modified to force the cell to produce fructose-6-phosphate which is an intermediate in the synthesis of GDP-fucose which meets the limitation of claim 17 (pg. 4, lines 21-22). Maertens teaches the engineered organism further comprises a glycosyltransferase which meets the limitation of claim 18 (pg. 15, lines 28-29). Maertens further teaches in Example 34, a Saccharomyces cerevisiae is modified to produce glucose-6-phosphate from sucrose, but because sucrose phosphorylase competes for sucrose with invertase, the genes coding for invertase activity are knocked out which meets the limitation of claim 21 (pg. 54, lines 3-6). Maertens teaches a gene encoding a phosphofructokinase is rendered non-functional, which meets the limitation of claim 22 (pg. 13, lines 18-22). Maertens teaches a biosynthesis pathway for 1,2 fucosyllactose, wherein glucose-1-P and fructose are utilized (pg. 80, Figure 10).
Maertens does not teach that the engineered microbe has a monosaccharide transporter for translocating a monosaccharide from the culture medium into the cell, wherein the transporter is encoded by the glf gene of Zymomonas mobilis, nor that the microorganism further produces an increased synthesis of phosphoenolpyruvate (PEP), nor engineered to overexpress pckA encoding a phosphoenolpyruvate carboxykinase or ppsA encoding a phosphoenolpyruvate synthase.
However, Chandran teaches PEP availability in the biosynthesis of shikimic acid (title). The highest titers and yields of shikimic acid biosynthesized from glucose in 1 L fermenter runs were achieved using E. coli SP1.lpts/pSC6.090B, which expressed both Z. mobilis glf-encoded glucose facilitator protein and Z. mobilis glk-encoded glucose kinase in a host deficient in the phosphoenolpyruvate:carbohydrate phosphotransferase system (abstract). Chandran teaches PTS-catalyzed phosphoryl group transfer from phosphoenolpyruvate drives (Figure 2) the transport of glucose into the microbial cytoplasm and phosphorylates glucose to form the glucose 6-phosphate required for glycolysis, wherein one molecule of phosphoenolpyruvate is converted into pyruvic acid for each molecule of glucose transported into the cytoplasm (pg. 808, col. 2, para 1). Chandran evaluated in one approach, pyruvic acid generated by PTS mediated glucose transport was recycled to phosphoenolpyruvate using amplified, ppsA-encoded phosphoenolpyruvate synthase (Figure 2), which converts pyruvic acid to phosphoenolpyruvate along with conversion of ATP to AMP and one molecule of inorganic phosphate (Figure 2), which meets the limitation of claim 24 (pg. 809, col. 1, para 2). Expenditure of phosphoenolpyruvate during glucose transport was avoided in a second approach by supplanting or augmenting PTS-mediated glucose transport with heterologous expression of the Zymomonas mobilis glf encoded glucose facilitator (Figure 2), wherein transport of glucose into the cytoplasm by Glf-mediated facilitated diffusion does not expend either phosphoenolpyruvate or ATP, though ATP is expended during the subsequent conversion of cytoplasmic glucose into glucose 6-phosphate catalyzed by glk-encoded glucokinase (Figure 2) (pg. 809, col. 1, para 2). Chandran teaches simultaneous operation of both Glf-mediated and PTS-mediated glucose transport in E. coli SP1.1/pSC5.112B led to one of the highest titers and yields of shikimic acid (pg. 813, col. 1, para 1).
Weisser also teaches functional expression of the glucose transporter glf leading to restoration of glucose and fructose uptake in E. coli mutants (title), further underlining this glucose facilitator’s ability of importing glucose and fructose in the medium.
Maertens, Chandran, and Weisser do not teach the engineered microorganisms were cultured in a medium wherein the main carbon source is a monosaccharide mixture comprising glucose and fructose.
However, Lendenmann teaches kinetics of simultaneous utilization of sugar mixtures by E. coli in continuous culture (title). Lendenmann teaches E. coli was cultured in a mixture of glucose and galactose, as well as mixtures of glucose and fructose (pg. 1494, col. 2, para 2; pg. 1497, col. 2, para 2). Lendenmann teaches growth with glucose-fructose mixtures resulted in a constant total flux through PTSs because both of these sugars are PTS sugars, and this may have led to a high and constant level of expression of PTS components enzyme I and protein Hpr, which are known to be synthesized constitutively, but when grown with PTS-carbohydrates leads to a 2-5-fold increase in the expression of these genes (pg. 1497, col. 2, para 4).
Therefore, it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claimed invention to utilize a genetically engineered microorganism with a reduced/diminished activity of consumption of a sugar phosphate and glycosyltransferase, as well as diminished expression of a gene encoding a protein competing with the biosynthesis of the desired carbohydrate, to produce said desired carbohydrate, 2’-fucosyllactose, as taught by Maertens, and modify the microbe with the glf gene derived from Z. mobilis, which would inherently produce enhanced synthesis of PEP relative to a wild-type, and culture said engineered microbe in a culture medium with a mixture of glucose and fructose as taught by Lendenmann. One of ordinary skill in the art would have been motivated to utilize a mixture of glucose and fructose, as these are the basic components of sucrose, which was the main carbon source of the engineered microbe taught by Maertens, as well as both monosaccharides can be imported by the glf gene as taught by Chandran and Weisser. Further, it would have been obvious to modify the engineered microbe taught by Maertens with a glucose transport facilitator (glf), which would reduce the cell’s energy expenditure (ATP) that is used in endogenous PTS system, as well as provide monosaccharides for biomass production and 1,2-fucosyllactose production, as outlined in Figure 10 taught by Maertens.
Claim 23 is rejected under 35 U.S.C. 103 as being unpatentable over Maertens, Lendenmann, Chandran, and Weisser as applied to claims 13, 14, 17, 18, 21-22, 24 above, and further in view of Jennewein et al. (WO 2010/142305 A1, cited in PTO-892 mailed 8/2/2024, hereinafter “Jennewein”).
Maertens teaches the engineered microorganism can comprise genes encoding for permeases that convert the activated saccharide into a specialty product (pg. 15, lines 20-26). Neither Maertens, Chandran, Weisser, nor Lendenmann teach the engineered microorganism comprises an exporter protein or permease that exports the desired carbohydrate.
However, Jennewein teaches engineered cells for the production of oligosaccharides comprising a protein of the sugar efflux transporter family (SET) (abstract). Jennewein teaches the overexpression of SET exporter proteins leads to efficient export of oligosaccharides, such as 3’-fucosyllactose (pg. 7, para 4; pg. 20, Example 3).
Therefore, it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claimed invention to genetically engineer a microorganism taught by Maertens with the glf gene derived from Z. mobilis taught by Chandran, and engineer the cell to overexpress a SET protein that exports the desired carbohydrate into the culture medium as taught by Jennewein, while culturing the engineered microbe in the carbon source mixture taught by Lendenmann. One of ordinary skill in the art would have been motivated to include a suitable export protein in the genetically engineered cell to efficiently export the desired carbohydrate for harvesting the sugar, without needing to disrupt the cell’s integrity with conventional centrifugation techniques that would lyse the cell as taught by Jennewein.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 13, 14, 17, 18, and 22-24 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 2, 5, 7, and 15-17 of U.S. Patent No. 11713475 B2 (‘475) in view of Chandran and Weisser.
Regarding instant claims 13 and 22, claim 1 of ‘475 recites a method for production of oligosaccharide of interest which comprises a galactose-β1,4-glucose moiety at its reducing end. The method comprises providing a genetically engineered microbial cell and cultivating in a mixture of glucose and fructose as a main carbon source which anticipates these limitations of instant claim 13. Claim 15 of ‘475 recites the microbial cell comprises a deletion or functional inactivation of a glucose-6-phosphate isomerase which anticipates the limitations of instant claims 13 and 22. Glucose-6-phosphate isomerase is a protein identified as leading to a consumption of intracellular sugar phosphate in instant claims 13 and 22. Claims 1, 5, and 7 of ‘475 recites the engineered cell comprises at least one glucose transporter for translocating glucose from the culture medium into the microbial cell's cytoplasm, and can be selected from diffusion proteins or glucose translocating permeases, and the said transporter is expressed or overexpressed.
‘475 does not recite the genetically engineered microbial cell further comprises a monosaccharide transporter that is encoded by the glf gene of Z. mobilis, nor that the microorganism further produces an increased synthesis of PEP.
However, Chandran teaches PEP availability in the biosynthesis of shikimic acid (title). The highest titers and yields of shikimic acid biosynthesized from glucose in 1 L fermenter runs were achieved using E. coli SP1.lpts/pSC6.090B, which expressed both Z. mobilis glf-encoded glucose facilitator protein and Z. mobilis glk-encoded glucose kinase in a host deficient in the phosphoenolpyruvate:carbohydrate phosphotransferase system (abstract). Chandran teaches PTS-catalyzed phosphoryl group transfer from phosphoenolpyruvate drives (Figure 2) the transport of glucose into the microbial cytoplasm and phosphorylates glucose to form the glucose 6-phosphate required for glycolysis, wherein one molecule of phosphoenolpyruvate is converted into pyruvic acid for each molecule of glucose transported into the cytoplasm (pg. 808, col. 2, para 1). Chandran evaluated in one approach, pyruvic acid generated by PTS mediated glucose transport was recycled to phosphoenolpyruvate using amplified, ppsA-encoded phosphoenolpyruvate synthase (Figure 2), which converts pyruvic acid to phosphoenolpyruvate along with conversion of ATP to AMP and one molecule of inorganic phosphate (Figure 2), which meets the limitation of claim 24 (pg. 809, col. 1, para 2). Expenditure of phosphoenolpyruvate during glucose transport was avoided in a second approach by supplanting or augmenting PTS-mediated glucose transport with heterologous expression of the Zymomonas mobilis glf encoded glucose facilitator (Figure 2), wherein transport of glucose into the cytoplasm by Glf-mediated facilitated diffusion does not expend either phosphoenolpyruvate or ATP, though ATP is expended during the subsequent conversion of cytoplasmic glucose into glucose 6-phosphate catalyzed by glk-encoded glucokinase (Figure 2) (pg. 809, col. 1, para 2). Chandran teaches simultaneous operation of both Glf-mediated and PTS-mediated glucose transport in E. coli SP1.1/pSC5.112B led to one of the highest titers and yields of shikimic acid (pg. 813, col. 1, para 1).
Weisser also teaches functional expression of the glucose transporter glf lead to restoration of glucose and fructose uptake in E. coli mutants (title), further underlining this glucose facilitator’s ability of importing glucose and fructose in the medium.
Therefore it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claimed invention to utilize the method recited in ‘475 of constructing a genetically engineered microbe for production of an oligosaccharide cultured in a monosaccharide mixture comprising glucose and fructose, wherein the glucose transporter recited in ‘475 is encoded by the glf gene derived from Z. mobilis as taught by Chandran. One of ordinary skill in the art would have been motivated to include a glucose transporter encoded by the glf gene as this monosaccharide transporter is known in the art to efficiently take up glucose and fructose as taught by Weisser. Furthermore, the genetically engineered microbe recited in ‘475 modified with the glf gene would inherently produce an increased synthesis of PEP relative to the wild-type, since the glucose diffused through the glucose facilitator would not require PEP for transport, thus increasing PEP abundance in the cell.
Regarding instant claim 14, claim 2 of ‘475 recites the oligosaccharide is selected from 2′-fucosyllactose, 3-fucosyllactose, 2′,3-difucosyllactose, 3′-sialyllactose, 6′-sialyllactose, 3-fucosyl-3′-sialyllactose, lacto-N-tetraose, lacto-N-neotetraose, lacto-N-fucopentaose I, lacto-N-fucopentaose II, lacto-N-fucopentaose III, lacto-N-fucopentaose V, lacto-N-difucosylhexose I, lacto-N-difucosylhexaose II, lacto-N-sialylpentaose LSTa, LSTb, LSTc.
Regarding instant claim 17, claim 1 of ‘475 recites the engineered cell comprises an UDP-galactose biosynthesis pathway.
Regarding instant claim 18, claim 1 of ‘475 recites the engineered cell comprises at least one β-1,4-galactosyltransferase being able to galactosylate free glucose to intracellularly produce lactose, which is a type of glycosyltransferase, thus anticipating the claim.
Regarding instant claim 23, claims 16 and 17 of ‘475 recites the engineered cell comprises an exporter protein or permease exporting the desired oligosaccharide from the cell, wherein the exporter is a sugar efflux transporter.
Response to Arguments
Applicant's arguments filed July 28, 2025 have been fully considered but they are not persuasive.
Regarding remarks directed to the 103 rejection, Applicant argues the primary reference does not describe a genetically engineered microbe grow on the monosaccharide mixture, nor that the microbe has a transporter encoded by the glf gene of Z. mobilis. Applicant argues the secondary references fail to remedy these deficiencies, because Lendenmann discloses E. coli was able to use all sugars which resulted in higher expression of components in the phosphotransferase system (PTS). However, it is noted this benefit was observed with non-PKS sugars (e.g. ribose). Tokuda merely teaches the glf gene for producing DOI, and none of the references describe an increased synthesis of PEP, and all together does not render the claimed method as obvious.
In response to applicant’s argument that there is no teaching, suggestion, or motivation to combine the references, the examiner recognizes that obviousness may be established by combining or modifying the teachings of the prior art to produce the claimed invention where there is some teaching, suggestion, or motivation to do so found either in the references themselves or in the knowledge generally available to one of ordinary skill in the art. See In re Fine, 837 F.2d 1071, 5 USPQ2d 1596 (Fed. Cir. 1988), In re Jones, 958 F.2d 347, 21 USPQ2d 1941 (Fed. Cir. 1992), and KSR International Co. v. Teleflex, Inc., 550 U.S. 398, 82 USPQ2d 1385 (2007). In this case, Maertens teaches a genetically modified organism recited in the claims, except for incorporating the glf gene, increased PEP synthesis, and culturing in a monosaccharide mixture of glucose and fructose. However, the newly applied Chandran reference teaches the glf gene, and its ability to transport glucose into the cell cytoplasm without the use of PEP from the PTS, therefore freeing up energy expenditure, as well as accumulating PEP in the cell. Furthermore, Chandran teaches by combining enhanced pckA expression and the glf gene, led to one of the highest titers and yields of shikimic acid. The newly applied Weisser reference further underscores glf’s ability to transport both glucose and fructose into the cell. Lendenmann teaches a method of culturing E. coli in a monosaccharide mixture of glucose and fructose, and discloses E. coli’s ability to utilize both of these sugars simultaneously. Regarding Applicant’s argument that Lendenmann did not teach the benefit with PTS sugars, the Examiner points to section ii) on page 1497, that describes E. coli’s growth on mixtures of glucose and fructose. Lendenmann teaches the specific excess uptake rate of fructose was very low during growth with glucose only, but growth with a mixture containing 10% fructose led to a drastic increase in the specific excess uptake rate of fructose to -1g • g-1 • h-1, and the value for this parameter increased with increasing proportions of fructose up to -1.8g • g-1 (Fig. 6). Lendenmann teaches with cells grown on glucose-ribose mixtures the specific excess glucose consumption rate depended on the composition of the mixture supplied in the feed, whereas the specific excess glucose consumption rate was independent of the composition of the mixture when the culture was grown on glucose-fructose mixtures (Fig. 6). Therefore, the combined references of Maertens, Chandran, Weisser, and Lendenmann render the claimed method obvious to one of ordinary skill in the art.
Applicant’s arguments with respect to the nonstatutory double patenting rejection over US Patent No. 11713475 for claims 13, 14, 17, 18, and 22-23 have been considered but are moot because the new ground of rejection does not rely on any reference applied in the prior rejection of record for any teaching or matter specifically challenged in the argument. (Remarks, pg. 9).
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JESSICA EDWARDS whose telephone number is (571)270-0938. The examiner can normally be reached M-F 8am-5pm 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, Louise Humphrey can be reached at (571) 272-5543. 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.
/JESSICA EDWARDS/
Examiner
Art Unit 1657
/LOUISE W HUMPHREY/Supervisory Patent Examiner, Art Unit 1657