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 .
DETAILED ACTION
1. Applicant’s hereby provisionally elect Group I encompassing claims 1-4, 11 and 12. Additionally, Applicants also hereby provisionally elect the specific mutation at position 434 of SEQ ID NO:1. If needed, Applicants further elect L434W as an example of such a specific species as recited in claim 2 (53).
Applicants understand that these species elections are being made to aid the Examiner in conducting a search and examination of the claimed subject matter and are not to be construed as limiting the scope of Applicants' claims. It is also Applicants' understanding that, if the elected subject matter is found to be allowable over the prior art, the search and examination will be expanded to cover other species, until it includes the full scope of the generic claims included in the elected group.
Additionally, as Applicants have elected the product claims of Group I, upon allowance of these claims, Applicants respectfully request rejoinder of the method of claims of Groups III and IV.
2. Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.03(a)). Rejoinder of the method of claims of Groups III and IV will be considered once the product claims becomes allowable.
As indicated in the restriction requirement mailed 12/3/25 - If restriction between product and process claims has been required, the following applies as per the rejoinder notice.
Where Applicant elects claims directed to a product, and the product claim is
subsequently found allowable, withdrawn process claims that depend from or otherwise
include all the limitations of the allowable product claim will be rejoined in accordance
with the Official Gazette notice dated March 26, 1996 (1184 O.G. 86; see also M.P.E.P.
821.04, In re Ochiai, and In re Brouwer). Process claims that depend from or otherwise
include all the limitations of the patentable product will be entered as a matter of right, if
the amendment is presented prior to final rejection or allowance, whichever is earlier.
Withdrawn process claims that are not commensurate in scope with an allowed product
claim will not be rejoined. To be allowable, the rejoined claims must meet all criteria for
patentability including the requirements of 35 U.S.C. 101, 102, 103, and 112.
3. Claims withdrawn:
Claims 5-10 & 13-20 are withdrawn from further consideration by the examiner, 37 CFR 1.142(b), as being drawn to a non-elected invention. Also withdrawn are the non-elected variants of the sequence of SEQ ID NO: 1.
3. Priority
Receipt is acknowledged of papers (foreign priority filed 3/31/21) submitted under 35 U.S.C. 119(a)-(d), which papers have been placed of record in the file.
4. Drawings
The drawings filed on 9/29/23 are acknowledged.
5. IDS(s) filed 9/29/23 & 3/5/24 are acknowledged. Signed copies of the IDS(s) are provided with this Office Action.
6. Specification
The specification has not been checked to the extent necessary to determine the presence of all possible minor errors. Applicant's cooperation is requested in correcting any errors of which applicant may become aware in the specification.
7. Written Description
Claims 1-4, 11 and 12 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112, first paragraph, as containing 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(s), at the time the application was filed, had possession of the claimed invention.
Claims 1-4, 11 and 12 are drawn to the following genus claims as noted in the example of claim 1.
Claim 1 is drawn to - A variant of a 3-methylcrotonic acid decarboxylase (MDC) showing an improved activity in converting 3-methylcrotonic acid into isobutene over the corresponding MDC from which it is derived and having an amino acid sequence as shown in SEQ ID NO:1 or an amino acid sequence having at least 55% sequence identity to SEQ ID NO:1, in which one or more amino acid residues at a position selected from the group consisting of positions 7, 17, 27, 33, 35, 45, 46, 48, 51, 140, 144, 183, 184, 185, 222, 227, 284, 285, 286, 287, 288, 289, 290, 292, 321, 322, 327, 329, 330, 331, 337, 338, 355, 365, 378, 380, 384, 387, 388, 389, 391, 392, 393, 394, 395, 419, 424, 425, 428, 429, 431, 432, 434, 436, 437, 438, 439, 443, 444, 446, 447, 448, 449, 451, 453, 457, 458, 459, 460, 462, 464, 465, 467, 468, 470 and 471 in the amino acid sequence shown in SEQ ID NO:1 or at a position corresponding to any of these positions, are substituted with another amino acid residue or deleted or wherein an insertion has been effected at one or more of these positions.
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).
MPEP § 2163 further states that if a biomolecule is described only by a functional characteristic, without any disclosed correlation between function and structure of the biomolecule, it is "not sufficient characteristic for written description purposes, even when accompanied by a method of obtaining the claimed biomolecule.”
“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.
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.
In University of California v. Eli Lilly & Co., 43 USPQ2d 1938, the Court of Appeals for the Federal Circuit has held that “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”. As indicated in MPEP § 2163, 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 that Applicant was in possession of the claimed genus. In addition, MPEP § 2163 states that 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 factors considered in the Written Description requirement are (1) level of skill and knowledge in the art, (2) partial structure, (3) physical and/or chemical properties, (4) functional characteristics alone or coupled with a known or disclosed correlation between structure and function, and the (5) method of making the claimed invention. Disclosure of any combination of such identifying characteristics that distinguish the claimed invention from other materials and would lead one of skill in the art to the conclusion that the applicant was in possession of the claimed species is sufficient." MPEP § 2163.
In the instant case, there is no description beyond the variant of a 3-methylcrotonic acid decarboxylase (MDC) showing an improved activity in converting 3-methylcrotonic acid into isobutene over the corresponding MDC from which it is the amino acid sequence as shown in SEQ ID NO:1 or an amino acid sequence having at least 84% sequence identity to SEQ ID NO:1, and the claimed substitutions. Applicants have provided the amino acid sequence of SEQ ID NO: 1, a sequence which is 490 amino acids in length and 76 variants/mutants thereof, which calculates to about 16% (76x100/490=15.51%) variation; which would indicate that they had possession of the claimed genus of an amino acid sequence having at least 55% sequence identity to SEQ ID NO:1.
The genus of polypeptides and the encoding polynucleotides required in the claimed invention is an extremely large structurally and functionally variable genus. While the argument can be made that the recited genus of polypeptides is adequately described by the disclosure of the structures of SEQ ID NO: 1, with specific structures having the associated function/activity, since one could use structural homology to isolate those polypeptides and the encoding polynucleotides recited in the claims in case of a rejoinder. The art clearly teaches the “Practical Limits of Function Prediction”:
(a) Devos et al., (Proteins: Structure, Function and Genetics, 2000, Vol. 41: 98-107), teach that the results obtained by analyzing a significant number of true sequence similarities, derived directly from structural alignments, point to the complexity of function prediction. Different aspects of protein function, including (i) enzymatic function classification, (ii) functional annotations in the form of key words, (iii) classes of cellular function, and (iv) conservation of binding sites can only be reliably transferred between similar sequences to a modest degree. The reason for this difficulty is a combination of the unavoidable database inaccuracies and plasticity of proteins (Abstract, page 98) and the analysis poses interesting questions about the reliability of current function prediction exercises and the intrinsic limitation of protein function prediction (Column 1, paragraph 3, page 99) and conclude that “Despite widespread use of database searching techniques followed by function inference as standard procedures in Bioinformatics, the results presented here illustrate that transfer of function between similar sequences involves more difficulties than commonly believed. Our data show that even true pair-wise sequence relations, identified by their structural similarity, correspond in many cases to different functions (column 2, paragraph 2, page 105). Our data show that even true pair-wise sequence relations, identified by their structural similarity, correspond in many cases to different functions (column 2, paragraph 2, page 105). Applicants’ are respectfully directed to the problems associated EC Classification in the section “Transferring the EC Classification enzyme to Non-Enzyme Comparisons”; pages 101-102 and Fig. 2a)-b), highlighting the structural and functional heterogeneity based on EC Classification numbers; as the stereo-specificity, substrate-specificity and catalytic properties vary widely.
(b) Whisstock et al., (Quarterly Reviews of Biophysics 2003, Vol. 36 (3): 307-340) also highlight the difficulties associated with “Prediction of protein function from protein sequence and structure”; “To reason from sequence and structure to function is to step onto much shakier ground”, closely related proteins can change function, either through divergence to a related function or by recruitment for a very different function, in such cases, assignment of function on the basis of homology, in the absence of direct experimental evidence, will give the wrong answer (page 309, paragraph 4), it is difficult to state criteria for successful prediction of function, since function is in principle a fuzzy concept. Given three sequences, it is possible to decide which of the three possible pairs is most closely related. Given three structures, methods are also available to measure and compare similarity of the pairs. However, in many cases, given three protein functions, it would be more difficult to choose the pair with most similar function, although it is possible to define metrics for quantitative comparisons of different protein sequences and structures, this is more difficult for proteins of different functions (page 312, paragraph 5), in families of closely related proteins, mutations usually conserve function but modulate specificity i.e., mutations tend to leave the backbone conformation of the pocket unchanged but to affect the shape and charge of its lining, altering specificity (page 313, paragraph 4), although the hope is that highly similar proteins will share similar functions, substitutions of a single, critically placed amino acid in an active-site residue may be sufficient to alter a protein’s role fundamentally (page 323, paragraph 1).
(c) This finding is reinforced in the following scientific teachings for specific proteins in the art that suggest, even highly structurally homologous polynucleotides and encoded polypeptides do not necessarily share the same function. For example, Witkowski et al., (Biochemistry 38:11643-11650, 1999), teaches that one conservative amino acid substitution transforms a b-ketoacyl synthase into a malonyl decarboxylase and completely eliminates b-ketoacyl synthase activity.
As stated above, no information beyond the characterization of variants as noted and the sequence of SEQ ID NO: 1 has been provided by the applicants’, which would indicate that they had possession of the claimed genus of polypeptides and the encoding polynucleotides. As the claimed genera of polypeptides having widely variable structures and associated function, since minor changes in structure may result in changes affecting function and no additional information (species/variant/mutant) correlating structure with function has been provided. Furthermore, “Possession may not be shown by merely describing how to obtain possession of members of the claimed genus or how to identify their common structural features” (See University of Rochester, 358 F.3d at 927, 69 USPQ2d at 1895).
Therefore, one skilled in the art cannot reasonably conclude that applicant had possession of the claimed invention at the time the instant application was filed. Applicants are referred to the revised guidelines concerning compliance with the written description requirement of U.S.C. 112, first paragraph, published in the Official Gazette and also available at www.uspto.gov.
8. Claim Rejections - 35 USC § 112 (second paragraph)
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.
Claim 2 is 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 pre-AIA the applicant regards as the invention.
Claim 2 (15) recite – “…an amino acid residue at position 122 in the amino acid sequence shown in SEQ ID NO: 1..”, is unclear as the specification provides “an amino acid residue at position 222 in the amino acid sequence shown in SEQ ID NO: 1..” correction is required.
Claim 2 (17) recite “an amino acid residue at position 284 in the amino acid sequence shown in SEQ ID NO: 1 or at a position corresponding to this position, is deleted or substituted with aspartate or glutamate or a proline…”.
Position 284 of SEQ ID NO: 1 is already a proline, and which will revert back to the wild-type. Deletion of ‘proline’ is suggested to overcome this rejection.
Claim 2 (58) recite “an amino acid residue at position 443 in the amino acid sequence shown in SEQ ID NO: 1 or at a position corresponding to this position, is deleted or substituted with histidine or an alanine, glycine, leucine, arginine, threonine or valine is inserted…”.
Position 443 of SEQ ID NO: 1 is already an arginine, and which will revert back to the wild-type. Deletion of ‘arginine’ is suggested to overcome this rejection.
Claim 2 (59) recite “an amino acid residue at position 444 in the amino acid sequence shown in SEQ ID NO: 1 or at a position corresponding to this position, is deleted or substituted with phenylalanine, isoleucine, leucine, methionine, asparagine, arginine, threonine or valine or a glutamate, glycine, histidine, lysine, leucine, asparagine, proline, arginine, serine, threonine or valine is inserted”.
Position 444 of SEQ ID NO: 1 is already an histidine, and which will revert back to the wild-type. Deletion of ‘histidine’ is suggested to overcome this rejection.
Claim 2 (61) recite “an amino acid residue at position 447 in the amino acid sequence shown in SEQ ID NO: 1 or at a position corresponding to this position, is deleted or substituted with phenylalanine, histidine, isoleucine, threonine or tryptophan or a lysine, leucine, proline or tyrosine is inserted..”
Position 447 of SEQ ID NO: 1 is already an lysine, and which will revert back to the wild-type. Deletion of ‘lysine’ is suggested to overcome this rejection.
9. US 20190322996 A1 is drawn to variants using a different organisms [Hypocrea atroviridis (SEQ ID NO: 1) or Streptomyces sp. 769 (SEQ ID NO: 14]; compared to variants Yersinia frederiksenii (SEQ ID NO: 1) of the present invention. Hence, no art rejection is made using this art.
US 10988752 B2 and US 10808237 B2 were also reviewed and no ODP rejection(s) were applicable.
10. No claim is allowed.
11. Any inquiry concerning this communication or earlier communications from the examiner should be directed to TEKCHAND SAIDHA whose telephone number is (571)272-0940. The examiner can normally be reached on M-F 8.00-5.30. 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, Robert B Mondesi can be reached on 408 918 7584. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300. Information regarding the status of an application may be obtained from the Patent Application Information Retrieval (PAIR) system. Status information for published applications may be obtained from either Private PAIR or Public PAIR. Status information for unpublished applications is available through Private PAIR only. For more information about the PAIR system, see http://pair-direct.uspto.gov. Should you have questions on access to the Private PAIR system, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative or access to the automated information system, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/TEKCHAND SAIDHA/
Primary Examiner, Art Unit 1652
Recombinant Enzymes, Hoteling
Telephone: (571) 272-0940
Fax: (571) 273-0940
Prosecution Insights