DETAILED ACTION
Claims 1, 3-6, 8, 11-17, and 20-26 are pending.
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claim Objections
Claims 5 and 11 are objected to because of the following informalities:
Claim 5 is objected to for lacking a period at the end of the claim.
In claim 11, --the group consisting of-- should be inserted after “from”.
Claim Rejections - 35 USC § 112
The following is a quotation 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 35 U.S.C. 112 (pre-AIA ), first paragraph:
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, 3-6, 8, 11-17, and 20-26 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter that was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for pre-AIA the inventor(s), at the time the application was filed, had possession of the claimed invention.
The claims require arabitol-phosphate dehydrogenases with at least 80% identity to SEQ ID NO:11.
Proteins with 80% identity to 357 amino acid long SEQ ID NO:11 would have 71 amino acid substitutions relative to SEQ ID NO:11.
The specification fails to describe any arabitol-phosphate dehydrogenase with at least 80% identity to SEQ ID NO:11, other than SEQ ID NO:11 itself.
The prior art describes a sorbitol dehydrogenase with 99.7% identity to SEQ ID NO:11 (GenBank OQR24129, 2017, www.ncbi.nlm.nih.gov/protein/OQR24129) and several dehydrogenases with 81.3% - 87.4% identity to SEQ ID NO:11 (e.g., GenBank KRK33310, 2015, www.ncbi.nlm.nih.gov/protein/KRK33310; GenBank ERJ77727, 2013, www.ncbi.nlm.nih.gov/protein/ERJ77727). None of these are described in the art or the instant specification as being arabitol-phosphate dehydrogenases.
The only proteins described in the prior art as being arabitol-phosphate dehydrogenases have 67.7% and 44.1% identity to SEQ ID NO:11 (SEQ ID NOS:69 and 70, respectively, from US 7,226,761):
US-09-908-744B-69
Sequence 69, US/09908744B
Patent No. 7226761
GENERAL INFORMATION
APPLICANT: Miasnikov Andrei
APPLICANT: Ojamo Heikki
APPLICANT: Povelainen Mira
APPLICANT: Gros Hakan
APPLICANT: Toivari Mervi
APPLICANT: Richard Peter
APPLICANT: Ruohonen Laura
APPLICANT: Koivuranta Kari
APPLICANT: Londesborough John
APPLICANT: Aristidou Aristos
APPLICANT: Penttila Merja
APPLICANT: Plazanet-Menut Claire
APPLICANT: Deutscher Josef
TITLE OF INVENTION: Manufacture of Five-Carbon Sugars and Sugar Alcohols
FILE REFERENCE: 1427.0010005
CURRENT APPLICATION NUMBER: US/09/908,744B
CURRENT FILING DATE: 2001-07-20
PRIOR APPLICATION NUMBER: PCT/FI01/00051
PRIOR FILING DATE: 2001-01-22
PRIOR APPLICATION NUMBER: US 09/488,581
PRIOR FILING DATE: 2000-01-21
PRIOR APPLICATION NUMBER: US 08/790,585
PRIOR FILING DATE: 1997-01-29
PRIOR APPLICATION NUMBER: US 08/368,395
PRIOR FILING DATE: 1995-01-03
PRIOR APPLICATION NUMBER: US 08/110,672
PRIOR FILING DATE: 1993-08-24
PRIOR APPLICATION NUMBER: US 07/973,325
PRIOR FILING DATE: 1992-11-05
NUMBER OF SEQ ID NOS: 75
SEQ ID NO 69
LENGTH: 352
TYPE: PRT
ORGANISM: Bacillus halodurans
Query Match 67.6%; Score 1248; Length 352;
Best Local Similarity 67.7%;
Matches 235; Conservative 46; Mismatches 66; Indels 0; Gaps 0;
Qy 7 MKAVVKSEAGYDNMSLQEIPVPEVKGKQVLMKVAYTGICGTDIHTFKGEYANAVTPLVLG 66
|| | | ||| |: :: ||| :||:|||||||||:||||||||| | ||:|||
Db 5 MKGVSKQAPGYDQMAFIDLSVPEATDDKVLIKVAYTGICGSDIHTFKGEYKNPTTPVVLG 64
Qy 67 HEFSGKVVAVGDEVTKVKPGDRVTSETTFDTCGECVYCKNKEYNLCENRSGIGTKANGSM 126
|||||:|| || ||||| |||||||||| |||| ||| |:|||| :| ||||: ||||
Db 65 HEFSGQVVEVGANVTKVKVGDRVTSETTFYVCGECDYCKEKQYNLCPHRKGIGTQQNGSM 124
Qy 127 ANYVLTREESVHVLPDNVSYKLAAMSEPLASCVHAMYQKTPFTLHDTVLIIGPGPMGLLS 186
||||| ||||:|:|||::||: |||||||| ||||||||: | ||::|:||||:||
Db 125 ANYVLAREESIHLLPDHLSYEGAAMSEPLACCVHAMYQKSHLELKDTIIIMGPGPIGLYL 184
Qy 187 LQIAKEIGAFTIVSGITKDSDRLEIAKELGADIVVDTQKEDLAKIVMEATNGVGVTKVYD 246
|||||||||| |::|||||: || :||:||||::||| ||||||:| | |:| || ||||
Db 185 LQIAKEIGAFVIMTGITKDAHRLALAKKLGADVIVDTMKEDLAKVVNEITDGYGVDKVYD 244
Qy 247 CSGATPAVNAALPLLKKGGTFQQVGLFAKPLNELDERTIIQHEITYVGSRSQNPYDWPIA 306
||| |||||:|||::| | | |||||| : :|| :||| || |:|||||||||||||
Db 245 ASGAVPAVNASLPLIRKQGQFIQVGLFANKMVDLDTESIIQREIEYIGSRSQNPYDWPIA 304
Qy 307 IHLEAKGAINEDKMVTKVFDLDHWREAFEAMMAGKELKVLIASNPDD 353
||| |||||| |:|:|| : | |||||: :| | |:||:| |||::
Db 305 IHLLAKGAINIDEMITKKYPLTEWREAFDKVMEGNEIKVMIESNPEE 351
US-09-908-744B-70
Sequence 70, US/09908744B
Patent No. 7226761
GENERAL INFORMATION
APPLICANT: Miasnikov Andrei
APPLICANT: Ojamo Heikki
APPLICANT: Povelainen Mira
APPLICANT: Gros Hakan
APPLICANT: Toivari Mervi
APPLICANT: Richard Peter
APPLICANT: Ruohonen Laura
APPLICANT: Koivuranta Kari
APPLICANT: Londesborough John
APPLICANT: Aristidou Aristos
APPLICANT: Penttila Merja
APPLICANT: Plazanet-Menut Claire
APPLICANT: Deutscher Josef
TITLE OF INVENTION: Manufacture of Five-Carbon Sugars and Sugar Alcohols
FILE REFERENCE: 1427.0010005
CURRENT APPLICATION NUMBER: US/09/908,744B
CURRENT FILING DATE: 2001-07-20
PRIOR APPLICATION NUMBER: PCT/FI01/00051
PRIOR FILING DATE: 2001-01-22
PRIOR APPLICATION NUMBER: US 09/488,581
PRIOR FILING DATE: 2000-01-21
PRIOR APPLICATION NUMBER: US 08/790,585
PRIOR FILING DATE: 1997-01-29
PRIOR APPLICATION NUMBER: US 08/368,395
PRIOR FILING DATE: 1995-01-03
PRIOR APPLICATION NUMBER: US 08/110,672
PRIOR FILING DATE: 1993-08-24
PRIOR APPLICATION NUMBER: US 07/973,325
PRIOR FILING DATE: 1992-11-05
NUMBER OF SEQ ID NOS: 75
SEQ ID NO 70
LENGTH: 343
TYPE: PRT
ORGANISM: Bacillus halodurans (deduced sequence)
Query Match 44.1%; Score 815; Length 343;
Best Local Similarity 46.3%;
Matches 158; Conservative 67; Mismatches 114; Indels 2; Gaps 2;
Qy 7 MKAVVKSEAGYDNMSLQEIPVPEVKGKQVLMKVAYTGICGTDIHTFKGEYANAVTPLVLG 66
|||:||:: | : ::|| | | || :|| |||:||:||||::| | | |: ||
Db 1 MKALVKTQHGTGHFAVQEKPEPTPGKHQVKIKVKYTGVCGSDIHTYEGHYPVA-APVTLG 59
Qy 67 HEFSGKVVAVGDEVTKVKPGDRVTSETTFDTCGECVYCKNKEYNLCENRSGIGTKANGSM 126
|||||::| :|: || |||||||||: ||:| || : :|||| :| |:| : :||
Db 60 HEFSGEIVELGEGVTGFNVGDRVTSETTYSICGKCSYCTSGDYNLCSHRKGLGNQQDGSF 119
Qy 127 ANYVLTREESVHVLPDNVSYKLAAMSEPLASCVHAMYQKTPFTLHDTVLIIGPGPMGLLS 186
| ||: |:||:| || | : |||:|||| | | || | |:: ||||:|||:
Db 120 AKYVIARQESLHHLPAGVDDRSAAMTEPLA-CTHHAIA KTSINKGDLVVVTGPGPIGLLA 178
Qy 187 LQIAKEIGAFTIVSGITKDSDRLEIAKELGADIVVDTQKEDLAKIVMEATNGVGVTKVYD 246
|:|| | |::|:: | ||: |||:| | :|||: |: ::| | |:| | | :
Db 179 AQVAKSHGGTVIITGLSNDQVRLKKAKEVGIDYAIDTQEVDIKELVSELTDGYGADVVLE 238
Qy 247 CSGATPAVNAALPLLKKGGTFQQVGLFAKPLNELDERTIIQHEITYVGSRSQNPYDWPIA 306
|||| || : ||:| | : ||||||:| : : ||| ||: |||||| | || |
Db 239 CSGAVPAAKQGIDLLRKKGQYAQVGLFAQPEIQFNFEKIIQKEISVVGSRSQKPADWEPA 298
Qy 307 IHLEAKGAINEDKMVTKVFDLDHWREAFEAMMAGKELKVLI 347
: | : :| :|| : : | :|: |: :|: :|||:
Db 299 LSLLNEKKVNAKTLVTHEYTISEWDKAYHAIKSGEAIKVLL 339
Thus, neither the prior art nor the specification describe any arabitol-phosphate dehydrogenase with at least 80% identity to SEQ ID NO:11, other than SEQ ID NO:11 itself.
Neither the prior art nor the specification describe motifs or domains and necessary and the sufficient structural elements of arabitol-phosphate dehydrogenases. The specification describes no structure as being required for arabitol-phosphate dehydrogenase activity.
The structural features that distinguish arabitol-phosphate dehydrogenases with 80% identity to SEQ ID NO:11 from other dehydrogenases with 80% identity to SEQ ID NO:11 are not described in the specification.
One of skill in the art would not recognize that Applicant was in possession of the necessary common attributes or features of the genus in view of the single disclosed species.
Since the disclosure fails to describe the common attributes that identify members of the genus, and because the genus is highly variant, SEQ ID NO:11 alone is insufficient to describe the claimed genus.
Hence, Applicant has not, in fact, described arabitol-phosphate dehydrogenases over the full scope of the claims, and the specification fails to provide an adequate written description of the claimed invention.
Therefore, given the lack of written description in the specification with regard to the structural and functional characteristics of the claimed compositions, Applicant does not appear to have been in possession of the claimed genus at the time this application was filed.
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 the second paragraph of 35 U.S.C. 112:
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 11, 14, 17 and 20-26 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 that the inventor or a joint inventor, or for pre-AIA the applicant, regards as the invention. Dependent claims are included in all rejections.
Claim 11 lacks antecedent basis for the limitations “the ER1 locus”, “the ER3 locus”, “the PDC1 locus”, “the pyrF locus”, “the TRP3 locus”, “the gpdIIA locus”, and “the gpdIIB locus” as these genes are not present in each and every yeast species. For example, ER1 and ER3, which encode erythrose reductases, are only present in erythritol-producing yeasts (Rzechonek et al, 2018, Crit. Rev. Biotechnol. 38:620-633; see pg 624, left column, ¶1).
It is unclear in claim 14 is the sequences in parenthesis are a required part of the claim or if they are merely optional.
In claim 17 it is unclear if “wherein fermentation of the substrate by the engineered yeast produces arabitol” is a method step or if it is merely stating what would happen if fermentation were to occur. Similarly, it is unclear if the fermentation conditions in dependent claims 20-25 are conditions applied to a method step or if they merely state conditions of a hypothetical fermentation. The rejections over claims 17 and 20-26 can be overcome by reciting fermentation as an active method step in claim 17 or by amending to make clear that fermentation is hypothetical.
Although SEQ ID NO:11 is known in the prior art as a sorbitol dehydrogenase (GenBank AOO74414, 2016, www.ncbi.nlm.nih.gov/protein/AOO74414), there is no motivation to transform a nucleic acid encoding it into yeast.
Conclusion
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Anne R. Kubelik, Ph.D., whose telephone number is (571) 272-0801. The examiner can normally be reached Monday through Friday, 9:00 am - 5:00 pm Eastern.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Amjad Abraham, can be reached at (571) 270-7058. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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.
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.
/Anne Kubelik/Primary Examiner, Art Unit 1663
Prosecution Insights