To 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 .
Claims 3-4, 6-8, 10-11,13, 15-16, and 18-19 are pending.
Claims 13, 15 and 19 remain withdrawn from further consideration as being drawn to non-elected groups (see Office actions mailed 10 September 2024 and 7 March 2025).
Claims 3-4, 6-8, 10-11, 16 and 18 are examined herein.
Nucleotide and/or Amino Acid Sequence Disclosures.
The application is now in compliance with the sequence rules.
Status of the claims
All rejections of claims 5, 9, 12 and 17 are moot in light of Applicant’s cancellation of the claims.
The objection to claims 9 and 18 objected to because of the minor informalities is withdrawn in light of Applicant’s amendment of the claims.
The rejection of claims 3-4, 6-8, 10, 16 and 18 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112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement is withdrawn in light of Applicant’s amendment of the claims.
The rejection of claims 3-4, 6-8, 10, 16 and 18 under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification does not reasonably provide enablement commensurate with the scope of the claims is withdrawn in light of Applicant’s amendment of the claims.
Claim Objections
Claim 3 is objected to because of the following informalities: the word “and” or “or” is missing from line 6, between the recitation of “(v) increasing plant height” and “(vi) increasing tiller number”; and on lines 7-8 the term “or” is missing between the recitation of “Gramineae” and “Brassicaceae” .
Claim 3 is further objected to because of the following informalities: please replace the recitation of “or”, at the end of item (i) with “and”. The alternatives listed are in part of a closed group as indicated by the language “consisting of” on line 9.
Claim 11 is objected to because of the following informalities: please replace the recitation of “or”, at the end of item (iii) with “and”. The alternatives listed are in part of a closed group as indicated by the language “consisting of” on line 2.
Appropriate correction is required.
“Use” Claim Rejection under 35 U.S.C. 112(b)/35 U.S.C. 101
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.
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.
MPEP 2173.05(q) “Use” Claims states:
Attempts to claim a process without setting forth any steps involved in the process generally raises an issue of indefiniteness under 35 U.S.C. 112(b) or pre-AIA 35 U.S.C. 112, second paragraph… “Use” claims that do not purport to claim a process, machine, manufacture, or composition of matter fail to comply with 35 U.S.C. 101.
Claim 4 is a “use claim” that sets forth a process of using an expression cassette or construct that overexpresses EmBP1. The claim however, as currently composed, does not comprise any process steps. In other words, it is not clear how this expression cassette or construct is used in a process. There are not method steps, for example, comprising transforming a plant with said cassette or construct. Based on MPEP 2173.05(q) these claims are to be rejected under 35 U.S.C. 35 112, second paragraph, as being indefinite. On alternative grounds these claims are further deemed to be improper process claims under 35 U.S.C. 101. This rejection is new, necessitated by Applicant’s amendment of claim 4.
Claim Rejections - 35 USC § 112
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 3-4, 6-8, 10-11, 16 and 18 remain 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. In light of Applicant’s amendment of the claims, this rejection has been modified from the one set forth in the previous Office action. Applicant’s arguments have been full considered but they are not persuasive.
Claim 3 is indefinite because it appears that the word “and” or “or” is missing from line 6, between the recitation of “(v) increasing plant height” and “(vi) increasing tiller number”. Thus it is not clear if the claim requires any one of the recited agronomic traits or requires all of the traits. Hence the metes and bounds of the claim are not clear. Claims 4, 6, 7, 8, 10, 11, 16 and 18 depend from claim 3, and as they do not comprise any language clarifying the meets and bounds of the claim from which they depend, are rejected on the grounds.
Claims 7, 10 and 18 recite apparent Markush groupings preceded by term “include”. The claims are considered indefinite because “include” is considered open language. Thus it is not clear what other traits or genes are included within the claimed groups. (See MPEP §2111.03 and §2173.05(h))
Response to Applicant’s arguments:
In the Remarks filed on 8 September 2025, on page 9, Applicant argues that their amendments, specifically to replace all recitations of “include” with “consist of”, has overcome the rejection.
This is not found persuasive.
Applicant has not in fact replaced all recitations of “include” and the amendment of claim 3 has raised a new ground for rejection under 35 U.S.C. 112(b). For these reasons the rejection is maintained.
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claim 11 is rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends. This rejection is new, necessitated by Applicant’s amendment of claim 3, which narrowed the scope of said claim.
Claim 11 depends from claim 3. Claim 3 requires that the EmBP1 is selected from a closed group of sequences that have at least 95% identity to SEQ ID NO: 1 or 3, or comprise the amino acid sequences of SEQ ID NO: 3. Claim 11 recites limitations drawn to the method of claim 3, wherein the EmBP1 is selected from a group of polypeptides with polypeptides with as littles as 80% identity to SEQ ID NO: 1, which have any number of changes relative to SEQ ID NO: 1, or which are functional fragments of SEQ ID NO: 1. Thus, claim 11 has a broader scope than claim 3 and fails to includes all the limitations of the claim upon which it depends.
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
The following is a quotation of the first paragraph of 35 U.S.C. 112(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.
Written Description
Claims 11 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 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. In light of Applicant’s amendment of the claims, this rejection has been modified from the one set forth in the previous Office action. Applicant’s arguments have been full considered but they are not persuasive.
Applicant claims a method of improving agronomic traits in a plant or preparing plants with improved agronomic traits, comprising increasing the expression of EmBP1, wherein the amino acid sequence of EmBP1 is selected from the group consisting of a (i) polypeptide with the amino acid sequence of SEQ ID NO: 1, (ii) a polypeptide having one or more deletions, insertions or substitutions relative to SEQ ID NO: 1 (iii) a polypeptide with as little as 80% sequence identity to SEQ ID NO: 1, or (iv) an active fragment of SEQ ID NO: 1.
Applicant has described SEQ ID NO: 1 as an EmBP1 protein (a bZIP transcription factor) derived from maize and SEQ ID NO: 2 as the coding region of an EmBP1 gene derived from maize (instant specification, Example 1).
Applicant has described SEQ ID NO: 3 as an EmBP1 protein derived from rice and SEQ ID NO: 4 as the coding region of an EmBP1 gene derived from rice (instant specification, Example 10).
SEQ ID NO: 3 has 80.9% identity to SEQ ID NO: 1.
Query Match 80.9%; Score 1613.5; Length 388;
Best Local Similarity 80.9%;
Matches 317; Conservative 24; Mismatches 38; Indels 13; Gaps 3;
Qy 1 MASSSDEQSKPPEPPAAA-----AVVTAAAPPQTHAEWVASLQAYYAAAGHPYAWPAQHL 55
|||||||| ||||||||| || |||| ||||| |||||||||||||||||||||
Db 1 MASSSDEQPKPPEPPAAAAVAGTAVATAAAAVPTHAEWAASLQAYYAAAGHPYAWPAQHL 60
Qy 56 MAAAAAGAHFGTPVPFPVYHPGAAAAYYAHASMAAGVPYPTCEAVPAVALP---TVPEGK 112
|||||||| :| |||||:||||||||||||||||||||||| ||: | | |||||
Db 61 MAAAAAGAPYGAPVPFPMYHPGAAAAYYAHASMAAGVPYPTAEAMAAAAAAAAGAVPEGK 120
Qy 113 GKGKGGGASPEKGSSGAPSGEDASRSDDSGSDESSETRDDDTDHKDSSAPKKRKSGNTSA 172
||||| |||||||| ||||:||||| ||||:|||:||||||||||||||||||||||||
Db 121 GKGKGAAASPEKGSSAAPSGDDASRSGDSGSEESSDTRDDDTDHKDSSAPKKRKSGNTSA 180
Qy 173 EGEPSQATVVRYAAVESPYPAKGRSASKLPVSAPGRAALPSATPNLNIGMDIWNASPALA 232
||||||||:| ||||||||| |||||||||||||||||||:||||||||:|:|: ||||
Db 181 EGEPSQATLVPYAAVESPYPLKGRSASKLPVSAPGRAALPNATPNLNIGIDLWSTPPALA 240
Qy 233 VPAVQGEVSPGLALARRDGVTQLDEREIKRERRKQSNRESARRSRLRKQQECEELARKVA 292
||| ||| |||||||||||| |||||:||||||||||||||||||||||||||||||||
Db 241 VPAGQGEASPGLALARRDGVAHLDERELKRERRKQSNRESARRSRLRKQQECEELARKVA 300
Qy 293 DLTTENSALRAELDNLKKACQDMEAENSRLLGGVADAQVPSVTTTLGMSIEPPKLQLQLQ 352
:|||||||||:||| |||||:||||||:||:| | : |:|||||||||: |
Db 301 ELTTENSALRSELDQLKKACEDMEAENTRLMGDKAQYKGPTVTTTLGMSIDSSK-----T 355
Qy 353 QHHDEEGQLHKKSSNNSNGNCAGGSHKPEANT 384
||||:|||||| ::|||||| |||||||||:
Db 356 QHHDDEGQLHKNTNNNSNGNYVGGSHKPEANS 387
Applicant describes transgenic rice and Arabidopsis plants comprising maize derived EmBP1 (i.e. SEQ ID NO: 2, which encodes SEQ ID NO: 1) transgenes and transgenic rice plants overexpressing EmBP1 which comprise rice derived EmBP1 (i.e. SEQ ID NO: 4, which encodes SEQ ID NO: 3) transgenes.
Applicant describes homologs of EmBP1 which appear to have been accessed from publicly available data sources, but does not disclose if they have the function of improving agronomic traits when their activity or expression is increased.
Applicant had not described any homologs of EmBP1 or any EmBP1 polypeptides with as little as 80% sequence identity to SEQ ID NO: 1 and which have the function of improving agronomic traits when their activity or expression is increased, aside from SEQ ID NO: 3.
Applicant has not disclosed any polypeptides which have any number of deletions, substitutions or insertions relative to the amino acid sequence of SEQ ID NO: 1 and which have the function of improving agronomic traits when their activity or expression is increased, aside from SEQ ID NO: 3.
Applicant has not described any fragments of SEQ ID NO: 1 which have the function of improving agronomic traits when their activity or expression is increased.
Applicant has not described any domains or motifs that are both necessary and sufficient for an EmBP1, homolog thereof, variant thereof or fragment thereof to have the function of improving agronomic traits when their activity or expression is increased or which would distinguish an EmBP1 polypeptide with as little as 80% sequence identity to SEQ ID NO: 1, homolog thereof, variant thereof or fragment thereof with the function of improving agronomic traits when their activity or expression is increased from polypeptides without said function.
Applicant has not provided a definition for homologs of EmBP1 which includes any lower bounds. Applicant defines “ homology” as the “level of two similarity” between two polynucleotides or polypeptides and provides an example of “high homology” as “at least 60% homology”(instant specification, page 8, lines 18-41). Thus homologs of EmBP1 encompass polypeptides with as little as 60% sequence identity to SEQ ID NO: 1.
Polypeptides with 60% identity to the 386 amino acid long SEQ ID NO: 1 encompass polypeptides with 154 amino acid substitutions relative to SEQ ID NO: 1. Polypeptides with 154 amino acid substitutions relative to SEQ ID NO: 1 encompass more than 20154 (2.28 X 10200) unique polypeptides.
Polypeptides with 80% identity to the 386 amino acid long SEQ ID NO: 1 encompass polypeptides with 77 amino acid substitutions relative to SEQ ID NO: 1. Polypeptides with 77 amino acid substitutions relative to SEQ ID NO: 1 encompass more than 2077 (1.51 X 10100) unique polypeptides.
Polypeptides which have any number of deletions, insertions or substitutions relative to SEQ ID NO: 1 would encompass polypeptides with 386 substitutions relative to SEQ ID NO: 1, as well as any number of shorter and longer polypeptides. This genus of encompassed polypeptides would be even larger than the two described above.
Thus, the genus of claimed polynucleotides, polypeptides and fragments thereof, is exceedingly vast. Applicant’s disclosure of two species (i.e. SEQ ID NOs: 1 and 3) does not constitute a sufficient number of representative species across this broad genus.
This deficiency is not remedied by the prior art. While there are numerous EmBP1 orthologs known in the art based on sequence identity, the prior art appears to be silent on whether these EmBP1 proteins have the function of improving agronomic traits when their activity or expression is increased (see Search Results for SEQ ID NOs: 1-2). The specification, on page 19, asserts that the phylogenetic tree shown in Figure 11 shows that there is a high level of conservation between the homologs from different species and thus “their functions are the same or similar”. However, phylogenetic trees provide no information regarding conservation of function or even structure. Rather, they show evolutionary relationships among the included genes, proteins or taxa. Species within a clade (e.g. sister species) are more closely related to each other than they are to species outside of the clade. Thus, even two distantly related species may be recovered as sister species, as long as they share a more common recent ancestor relative to other species included in the analysis or relative to the outgroup. Such analyses are further complicated by the presence of paralogs and genome duplication, as polyploidy is common in plants.
Furthermore, Applicant has not described the structures (e.g. domains or motifs) that are sufficient and necessary for an EmBP1 protein to confer improved agronomic traits when their activity or expression is increased such that one would not be able to envision which members of the claimed genus of polynucleotides, polypeptides and fragments have the required function and which do not. Applicant has also failed to describe any molecules that interact with EmBP1 and which, when up-regulated, increase expression or activity of EmBP1.
The prior art does not remedy this deficiency. The basic structure of bZIP transcription factors and EmBP1 (isolated initially from wheat) have been known for some time. Like other bZIP transcription factors, which are implicated in a variety of stress responses, EmBP1 comprises a conserved basic region which binds to sequence specific DNA and a conserved region of leucine repeats (i.e. leucine zipper) that mediates dimerization, along with glutamine-rich, proline-rich, and acidic-rich regions (Nieva et al, in J.H. Cherry et al (eds), Plant Tolerances to Abiotic Stresses in Agriculture: Role of Genetic Engineering, 157-180; page 166, second paragraph; page 170, paragraphs 3-4; page 171, paragraph 2; Guo et al, 2024, Plants 13: 2058, pages 2-3, “Structure of bZIP TFs” ). Guiltinan et al (1994, Plant Molecular Biology 26: 1041-1053) discloses a minimal domain fragment of approximately 60 amino acid residues as the smallest EmBP1 polypeptide that binds DNA (page 1048, column 2, “Minimal Domain”). However, other prior art discloses that transforming tobacco plants with a deletion variation of EmBP1 comprising just the DNA binding and dimerization domains, under the control of the CaMV promoter, led to tobacco plants with reductions in photosynthesis and growth, at least in low-light conditions (Eckardt et al, 1998, Plant Molecular Biology 38: 539-549; page 540, column 1, last paragraph; page 547, second column, second paragraph). Therefore, while it appears that the binding and dimerization domains are necessary for the function of DNA binding, they are not sufficient to confer the function of improved agronomic traits with increased expression or activity of EmBP1.
Thus, 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 disclosed species. Since the disclosure fails to describe the common attributes that identify members of the genus, and because the genus is highly diverse, SEQ ID NOs: 1 and 3 are insufficient to describe the claimed genus.
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.
Scope of enablement
Claims 11 is rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for methods of improving agronomic traits in plants by overexpressing polynucleotides encoding polypeptides with at least 95 % sequence identity to SEQ ID NOs: 1 or 3, does not reasonably provide enablement for methods of improving agronomic traits in plants by increasing the activity or expression of polynucleotides which encode a polypeptide with as little as 80% sequence identity to SEQ ID NO: 1, polynucleotides encoding a polypeptide having one or more deletions, insertions or substitutions relative to SEQ ID NO: 1, or polynucleotides encoding a fragment of SEQ ID NO: 1 of any length. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to use the invention commensurate in scope with these claims. In light of Applicant’s amendment of the claims, this rejection has been modified from the one set forth in the previous Office action. Applicant’s arguments have been full considered but they are not persuasive.
Applicant claims a method of improving agronomic traits in a plant or preparing plants with improved agronomic traits, comprising increasing the expression of EmBP1, wherein the amino acid sequence of EmBP1 is selected from the group consisting of a (i) polypeptide with the amino acid sequence of SEQ ID NO: 1, (ii) a polypeptide having one or more deletions, insertions or substitutions relative to SEQ ID NO: 1 (iii) a polypeptide with as little as 80% sequence identity to SEQ ID NO: 1, or (iv) an active fragment of SEQ ID NO: 1.
Applicant teaches that SEQ ID NO: 1 is an EmBP1 protein (a bZIP transcription factor) derived from maize and that SEQ ID NO: 2 is the coding region of an EmBP1 gene derived from maize (instant specification, Example 1).
Applicant teaches that SEQ ID NO: 3 is an EmBP1 protein derived from rice and that SEQ ID NO: 4 is the coding region of an EmBP1 gene derived from rice (instant specification, Example 10).
SEQ ID NO: 3 has 80.9% identity to SEQ ID NO: 1.
Query Match 80.9%; Score 1613.5; Length 388;
Best Local Similarity 80.9%;
Matches 317; Conservative 24; Mismatches 38; Indels 13; Gaps 3;
Qy 1 MASSSDEQSKPPEPPAAA-----AVVTAAAPPQTHAEWVASLQAYYAAAGHPYAWPAQHL 55
|||||||| ||||||||| || |||| ||||| |||||||||||||||||||||
Db 1 MASSSDEQPKPPEPPAAAAVAGTAVATAAAAVPTHAEWAASLQAYYAAAGHPYAWPAQHL 60
Qy 56 MAAAAAGAHFGTPVPFPVYHPGAAAAYYAHASMAAGVPYPTCEAVPAVALP---TVPEGK 112
|||||||| :| |||||:||||||||||||||||||||||| ||: | | |||||
Db 61 MAAAAAGAPYGAPVPFPMYHPGAAAAYYAHASMAAGVPYPTAEAMAAAAAAAAGAVPEGK 120
Qy 113 GKGKGGGASPEKGSSGAPSGEDASRSDDSGSDESSETRDDDTDHKDSSAPKKRKSGNTSA 172
||||| |||||||| ||||:||||| ||||:|||:||||||||||||||||||||||||
Db 121 GKGKGAAASPEKGSSAAPSGDDASRSGDSGSEESSDTRDDDTDHKDSSAPKKRKSGNTSA 180
Qy 173 EGEPSQATVVRYAAVESPYPAKGRSASKLPVSAPGRAALPSATPNLNIGMDIWNASPALA 232
||||||||:| ||||||||| |||||||||||||||||||:||||||||:|:|: ||||
Db 181 EGEPSQATLVPYAAVESPYPLKGRSASKLPVSAPGRAALPNATPNLNIGIDLWSTPPALA 240
Qy 233 VPAVQGEVSPGLALARRDGVTQLDEREIKRERRKQSNRESARRSRLRKQQECEELARKVA 292
||| ||| |||||||||||| |||||:||||||||||||||||||||||||||||||||
Db 241 VPAGQGEASPGLALARRDGVAHLDERELKRERRKQSNRESARRSRLRKQQECEELARKVA 300
Qy 293 DLTTENSALRAELDNLKKACQDMEAENSRLLGGVADAQVPSVTTTLGMSIEPPKLQLQLQ 352
:|||||||||:||| |||||:||||||:||:| | : |:|||||||||: |
Db 301 ELTTENSALRSELDQLKKACEDMEAENTRLMGDKAQYKGPTVTTTLGMSIDSSK-----T 355
Qy 353 QHHDEEGQLHKKSSNNSNGNCAGGSHKPEANT 384
||||:|||||| ::|||||| |||||||||:
Db 356 QHHDDEGQLHKNTNNNSNGNYVGGSHKPEANS 387
Applicant describes transgenic rice and Arabidopsis plants comprising maize derived EmBP1 (i.e. SEQ ID NO: 2, which encodes SEQ ID NO: 1) transgenes and transgenic rice plants overexpressing EmBP1 which comprise rice derived EmBP1 (i.e. SEQ ID NO: 4, which encodes SEQ ID NO: 3) transgenes.
Applicant describes homologs of EmBP1 which appear to have been accessed from publicly available data sources, but does not disclose if they have the function of improving agronomic traits when their activity or expression is increased.
Applicant had not described any homologs of EmBP1 or any EmBP1 polypeptides with as little as 80% sequence identity to SEQ ID NO: 1 and which have the function of improving agronomic traits when their activity or expression is increased, aside from SEQ ID NO: 3.
Applicant has not disclosed any polypeptides which have any number of deletions, substitutions or insertions relative to the amino acid sequence of SEQ ID NO: 1 and which have the function of improving agronomic traits when their activity or expression is increased, aside from SEQ ID NO: 3.
Applicant has not described any fragments of SEQ ID NO: 1 which have the function of improving agronomic traits when their activity or expression is increased.
Applicant has not described any domains or motifs that are both necessary and sufficient for an EmBP1, homolog thereof, variant thereof or fragment thereof to have the function of improving agronomic traits when their activity or expression is increased or which would distinguish an EmBP1 polypeptide with as little as 80% sequence identity to SEQ ID NO: 1, homolog thereof, variant thereof or fragment thereof with the function of improving agronomic traits when their activity or expression is increased from polypeptides without said function.
Applicant has not provided a definition for homologs of EmBP1 which includes any lower bounds. Applicant defines “ homology” as the “level of two similarity” between two polynucleotides or polypeptides and provides an example of “high homology” as “at least 60% homology”(instant specification, page 8, lines 18-41). Thus homologs of EmBP1 encompass polypeptides with as little as 60% sequence identity to SEQ ID NO: 1.
As explained above under the U.S.C. 112(a) written description rejection, the polypeptides and fragments thereof required by the claimed methods constitute a vast genus which applicant does not teach across the full scope of the claims.
The specification fails to provide guidance for how to make, polynucleotides which encode a polypeptide with as little as 80% sequence identity to SEQ ID NO: 1, polynucleotides encoding any polypeptide derived from SEQ ID NO: 1 with any number of deletions, insertions or substitutions, or polynucleotides encoding a fragment of SEQ ID NO: 1 of any length and which have the function of improving agronomic traits when their activity or expression or increased, aside from SEQ ID NO: 3.
The instant specification fails to provide guidance for which amino acids of SEQ ID NO:1 can be altered and to which other amino acids, and which amino acids must not be changed, to maintain the function of improving agronomic traits. The specification also fails to provide guidance for which amino acids can be deleted and which regions of the protein can tolerate insertions and still produce a functional transcription factor. The specification fails to provide what minimal fragment of SEQ ID NO: 1 is needed to maintain the function of improving agronomic traits.
Applicant teaches that SEQ ID NO: 1 is an EmBP1 protein (a bZIP transcription factor) derived from maize and that SEQ ID NO: 2 is the coding region of an EmBP1 gene derived from maize (instant specification, Example 1). However, the specification does not teach any structures, motifs or amino acid resides that are necessary to confer the function of improving agronomic traits with increased activity or expression. The prior art teaches that bZIP transcription factors, which are implicated in a variety of stress responses, comprises a conserved basic region which binds to sequence specific DNA and a conserved region of leucine repeats (i.e. leucine zipper) that mediates dimerization, along with glutamine-rich, proline-rich, and acidic-rich regions (Nieva et al, in J.H. Cherry et al (eds), Plant Tolerances to Abiotic Stresses in Agriculture: Role of Genetic Engineering, 157-180; page 166, second paragraph; page 170, paragraphs 3-4; page 171, paragraph 2; Guo et al, 2024, Plants 13: 2058, pages 2-3, “Structure of bZIP TFs” ). Guiltinan et al (1994, Plant Molecular Biology 26: 1041-1053) teaches that a minimal domain fragment of approximately 60 amino acid residues as the smallest EmBP1 polypeptide that binds DNA (page 1048, column 2, “Minimal Domain”). However, other prior art teaches that transforming tobacco plants with a deletion variation of EmBP1 comprising just the DNA binding and dimerization domains, under the control of the CaMV promoter, led to tobacco plants with reductions in photosynthesis and growth, at least in low-light conditions (Eckardt et al, 1998, Plant Molecular Biology 38: 539-549; page 540, column 1, last paragraph; page 547, second column, second paragraph). Therefore, while it appears that the binding and dimerization domains are necessary for the function of DNA binding, they are not sufficient to confer the function of improved agronomic traits with increased expression or activity of EmBP1.
The specification teaches that fragments, derivatives and analogs of EmBP1 can be made by deletions, substitution or insertions in SEQ ID NO: 1, however they do not teach which residues can be altered and which must remain unchanged for the claimed function to remain unchanged (instant specification, page 7, lines 30, to page 8 lines 17).
Thus, from the guidance in the specification, it would appear that one of skill in the art would need to make the claimed polypeptides and polynucleotides by making random nucleotide and amino acid substitutions, which would be unpredictable.
While proteins are fairly tolerant to mutations resulting in single amino acid changes, increasing the number of substitutions additively increases the probability that the protein will be inactivated (Guo et al, 2004, Proc. Natl. Acad. Sci. USA 101: 9205-9210; pg 9209, right column, paragraph 2). Given the vast number of polynucleotides and polypeptides encompassed by the claims, making and assaying even a representative sample to find any that confer improved agronomic traits with increased activity or expression would entail undue experimentation.
Likewise, Applicant has not taught any homologs of EmBP1 that have the function of improving agronomic traits with increased activity or expression, aside from SEQ ID NO: 3. Applicant has not taught from which plants such a homolog can be isolated. The specification states that such homologs can be isolated from other plants, especially those related to maize (page 8, lines 26-34). The specification, on page 19, asserts that the phylogenetic tree shown in Figure 11 shows that there is a high level of conservation between the homologs from different species and thus “their functions are the same or similar”. However, phylogenetic trees provide no information regarding conservation of function or even structure. Rather, they show evolutionary relationships among the included genes, proteins or taxa. Species within a clade (e.g. sister species) are more closely related to each other than they are to species outside of the clade. Thus, even two distantly related species may be recovered as sister species, as long as they share a more common recent ancestor relative to other species included in the analysis or relative to the outgroup. While there are numerous EmBP1 orthologs known in the art based on sequence identity, the prior art appears to be silent on whether these EmBP1 proteins have the function of improving agronomic traits when their activity or expression is increased (see Search Results for SEQ ID NOs: 1-2). Thus one would be reduced to isolating and assaying each homolog for activity, which would also entail undue experimentation.
Thus extensive teachings are required for making polynucleotides which encode a polypeptide with as little as 80% sequence identity to SEQ ID NO: 1, polynucleotides encoding any polypeptide derived from SEQ ID NO: 1 with any number of deletions, insertions or substitutions, or polynucleotides encoding a fragment of SEQ ID NO: 1 of any length and using said polynucleotides, polypeptides and fragments thereof in a method for improving agronomic traits. These teachings are not provided for by specification. The specification also fails to overcome the unpredictability in the art.
Undue experimentation would have been required by one skilled in the art to develop and evaluate for methods of improving agronomic traits in plants by increasing the activity or expression of polynucleotides which encode a polypeptide with as little as 80% sequence identity to SEQ ID NO: 1, polynucleotides encoding any polypeptide derived from SEQ ID NO: 1 with any number of deletions, insertions or substitutions, or polynucleotides encoding a fragment of SEQ ID NO: 1 of any length and using said polynucleotides, polypeptides and fragments thereof in a method for improving agronomic traits
As the specification does not describe the modification of a polynucleotide conferring improved agronomic traits or a polypeptide encoded by said nucleic acid, undue trial and error experimentation would be required to screen through the myriad of nucleic acids and polypeptides encompassed by the claims, to identify those capable of use with the claimed methods.
Given the claim breath, unpredictability in the art, undue experimentation, and lack of guidance in the specification as discussed above, the instant invention is not enabled throughout the full scope of the claims.
Response to Applicant’s arguments:
In the Remarks filed 8 September 2025, on page 10, Applicant argues that the claim amendments to limit the amino acid sequence to polypeptides comprising a sequence with at least 95% identity to SEQ ID NO: 1 or 3 overcomes the written description and enablement rejections under 35 U.S.C. 112(a).
This is not found persuasive.
Claim 11 has not been amended to limit the claimed polypeptides to polypeptides comprising a sequence with at least 95% identity to SEQ ID NO: 1 or 3.
Therefore, the rejection is maintained.
Claim Rejections - 35 USC § 103
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 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.
Claims 3-4, 6-8, 10-11, 16 and 18 are rejected under 35 U.S.C. 103 as being unpatentable over Cai et al (CN104725493A; published 2015-06-24) in view of UniProt Accession B4FC61 (2018, uniprot.org/uniprotkb/B4FC61/entry, version 62; integrated 2008-09-23). In light of Applicant’s amendment of the claims, this rejection has been modified from the one set forth in the previous Office action. Applicant’s arguments have been full considered but they are not persuasive.
The claims are broadly drawn to a method of improving agronomic traits selected from increasing photosynthesis efficiency, regulating the expression of photosynthetic genes, increasing yield, increasing biomass, increasing plant height, or increasing tiller number; comprising increasing the expression of EmBP1 in a Gramineae or Brassicaceae, wherein the EmBP1 polypeptide has at least 95% sequence identity to SEQ ID NO: 1 or 3 (claim 3); the method of claim 3, using an expression cassette or construct that overexpresses EmBP1 (claim 4); the method of claim 3, wherein the Gramineae is selected from rice or maize (among others) (claim 6); the method of claim 3, wherein the plant is a Gramineae and the improved trait is seed weight (claim 7); the method of claim 3, wherein, improving photosynthetic efficiency includes: increasing C02 absorption rate, increasing electron transfer efficiency, increasing maximum electron transfer rate, increasing Rubisco maximum catalytic efficiency, increasing chlorophyll content, increasing maximum quantum yield, increasing the aperture beam size of the reaction center, or improving the level of the electron transport chain (claim 10); the method of claim 3, wherein EmBP1 is a polypeptide having the amino acid sequence of SEQ ID NO: 1 (claim 11); the method of claim 8, wherein the EmBP1 or homolog thereof regulates the promoter of the photosynthetic genes (claim 16); the method according to claim 3, wherein the photosynthetic genes include PsbR3, RbcS3, FBA1, FBPse, Fdl, PsaN and/orCP29 (claim 18).
Cai et al teaches a method for improving a gramineous plant (i.e. a Gramineae) comprising increasing the expression of an OsbZIP34 protein or a homolog thereof (claim 1). Cai et al teaches said method where in the yield or 1000-grain weight of the seeds of the gramineous plant are increased (claim 2). Cai et al teaches overexpressing OsbZIP34 by transformation of a rice plant with an expression construct (see translated document, page 11, “Agrobacterium-mediated rice transformation” and “Construction of overexpression vector of OsbZIP34”; page 14, Example 4). Cai et al further teaches that EmBP-1 from maize has high homology to OsbZIP34 (see translated document, pages 12-13, Example 1).
Cai et al teaches a maize EmBP-1 protein with 99.3% similarity to instant SEQ ID NO: 1:
Query Match 99.3%; Score 1981; Length 386;
Best Local Similarity 99.5%;
Matches 384; Conservative 0; Mismatches 2; Indels 0; Gaps 0;
Qy 1 MASSSDEQSKPPEPPAAAAVVTAAAPPQTHAEWVASLQAYYAAAGHPYAWPAQHLMAAAA 60
||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MASSSDEQSKPPESPAAAAVVTAAAPPQTHAEWVASLQAYYAAAGHPYAWPAQHLMAAAA 60
Qy 61 AGAHFGTPVPFPVYHPGAAAAYYAHASMAAGVPYPTCEAVPAVALPTVPEGKGKGKGGGA 120
|||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 AGAHFGIPVPFPVYHPGAAAAYYAHASMAAGVPYPTCEAVPAVALPTVPEGKGKGKGGGA 120
Qy 121 SPEKGSSGAPSGEDASRSDDSGSDESSETRDDDTDHKDSSAPKKRKSGNTSAEGEPSQAT 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 SPEKGSSGAPSGEDASRSDDSGSDESSETRDDDTDHKDSSAPKKRKSGNTSAEGEPSQAT 180
Qy 181 VVRYAAVESPYPAKGRSASKLPVSAPGRAALPSATPNLNIGMDIWNASPALAVPAVQGEV 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 VVRYAAVESPYPAKGRSASKLPVSAPGRAALPSATPNLNIGMDIWNASPALAVPAVQGEV 240
Qy 241 SPGLALARRDGVTQLDEREIKRERRKQSNRESARRSRLRKQQECEELARKVADLTTENSA 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 SPGLALARRDGVTQLDEREIKRERRKQSNRESARRSRLRKQQECEELARKVADLTTENSA 300
Qy 301 LRAELDNLKKACQDMEAENSRLLGGVADAQVPSVTTTLGMSIEPPKLQLQLQQHHDEEGQ 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 LRAELDNLKKACQDMEAENSRLLGGVADAQVPSVTTTLGMSIEPPKLQLQLQQHHDEEGQ 360
Qy 361 LHKKSSNNSNGNCAGGSHKPEANTTR 386
||||||||||||||||||||||||||
Db 361 LHKKSSNNSNGNCAGGSHKPEANTTR 386
Cai et al does not teach a maize EmBP-1 protein with 100% sequence identity to instant SEQ ID NO: 1.
UniProt Accession B4FC61 teaches an EmBP-1 protein with 100% identity to instant SEQ ID NO: 1:
Query Match 100.0%; Score 1995; Length 386;
Best Local Similarity 100.0%;
Matches 386; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MASSSDEQSKPPEPPAAAAVVTAAAPPQTHAEWVASLQAYYAAAGHPYAWPAQHLMAAAA 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MASSSDEQSKPPEPPAAAAVVTAAAPPQTHAEWVASLQAYYAAAGHPYAWPAQHLMAAAA 60
Qy 61 AGAHFGTPVPFPVYHPGAAAAYYAHASMAAGVPYPTCEAVPAVALPTVPEGKGKGKGGGA 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 AGAHFGTPVPFPVYHPGAAAAYYAHASMAAGVPYPTCEAVPAVALPTVPEGKGKGKGGGA 120
Qy 121 SPEKGSSGAPSGEDASRSDDSGSDESSETRDDDTDHKDSSAPKKRKSGNTSAEGEPSQAT 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 SPEKGSSGAPSGEDASRSDDSGSDESSETRDDDTDHKDSSAPKKRKSGNTSAEGEPSQAT 180
Qy 181 VVRYAAVESPYPAKGRSASKLPVSAPGRAALPSATPNLNIGMDIWNASPALAVPAVQGEV 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 VVRYAAVESPYPAKGRSASKLPVSAPGRAALPSATPNLNIGMDIWNASPALAVPAVQGEV 240
Qy 241 SPGLALARRDGVTQLDEREIKRERRKQSNRESARRSRLRKQQECEELARKVADLTTENSA 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 SPGLALARRDGVTQLDEREIKRERRKQSNRESARRSRLRKQQECEELARKVADLTTENSA 300
Qy 301 LRAELDNLKKACQDMEAENSRLLGGVADAQVPSVTTTLGMSIEPPKLQLQLQQHHDEEGQ 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 LRAELDNLKKACQDMEAENSRLLGGVADAQVPSVTTTLGMSIEPPKLQLQLQQHHDEEGQ 360
Qy 361 LHKKSSNNSNGNCAGGSHKPEANTTR 386
||||||||||||||||||||||||||
Db 361 LHKKSSNNSNGNCAGGSHKPEANTTR 386
Examiner notes that a polypeptide, such as that of UniProt Accession B4FC61 makes obvious all the polynucleotide sequences which encode said polypeptide.
At the time of filing, it would have been prima facie obvious to one of ordinary skill in the art to modify the method taught by Cai et al to overexpress the EmBP-1 polypeptide taught by UniProt Accession B4FC61. One would have been motivated to do so because claim 1 of Cai et al recites “a OsbZIP34 protein or a homolog thereof” and Cai et al teach that EmBP-1 from maize is a homolog of OsbZIP34. Further, Cai et al teach a maize EmBP-1 with over 99% identity to instant SEQ ID NO: 1, and by extension over 99% identity to the EmBP-1 protein taught by UniProt Accession B4FC61. Thus substituting the EmBP-1 of UniProt Accession B4FC61 for the homolog of OsbZIP34 protein taught by Cai et al (i.e. the maize EmBP-1 of Cai et al) would be a substitution of equivalents. One would have a reasonable expectation of success given the teachings of Cai et al, the routine nature of overexpressing a heterologous protein by transformation, and given the high skill level of one having ordinary skill in the art.
Regarding the limitations of the claims drawn to increased seed yield, the affected photosynthetic genes, the binding domains, the modes of action, etc., these constitute intended results and inherent properties of the claimed invention, by applicant’s own admission (see Examples in the specification which detail the results of Applicants’ experiments). Thus, as the combined prior art references make obvious all the active method steps and teach a polypeptide with 100% sequence identity to instant SEQ ID NO: 1, the combined prior art references also make obvious the intended results and inherent properties which flow from practicing said active method steps.
Response to Applicant’s arguments:
In the Remarks filed 8 September 2025, on pages 10-12, that the claimed polypeptide of Cai et al (OsbZIP34) has low sequence homology to the maize bzip polypeptide taught there in (ZmEmbp-1a) and similarity low homology to instant SEQ ID NO: 1. Applicant further argues that Cai does not teach or suggest that ZmEmbp-1a would increase yield (1000 grain weight). Applicant continues that UniProt accession B4FC6 does not describe the function of the polypeptide taught therein and one would not be able to reasonably predict that combining the teachings of Cai et al with the teachings of UniProt accession B4FC6 would result in a plant with improved agronomic traits, as claimed by the instant invention.
This is not found persuasive.
Cai et al teaches a method for improving (e.g. increasing yield) a gramineous plant comprising increasing the expression of an OsbZIP34 protein or a homolog thereof. Cai et al further explicitly teaches that EmBP-1 from maize is such a homolog. The level of homology between these two homologs is irrelevant, because we do not rely on homology between the two proteins to select the maize homolog. Rather, one would select it based on Cai’s teachings. Substituting the maize homolog for the rice protein would be obvious to try given the explicit teachings of Cai et al. Further, one does not need a guarantee of success, just a reasonable expectation of success.
Further, as explained above, Cai et al teach a maize EmBP-1 with over 99% identity to instant SEQ ID NO: 1, and by extension over 99% identity to the EmBP-1 protein taught by UniProt Accession B4FC61. Thus substituting the EmBP-1 of UniProt Accession B4FC61 for the homolog of OsbZIP34 protein taught by Cai et al (i.e. the maize EmBP-1 of Cai et al) would be a substitution of equivalents. One would have a reasonable expectation that these two proteins would have similar functions given their nearly identical sequences (over 99%) and membership in the same family of proteins.
For these reasons, the rejection is maintained.
Conclusion
No claims are allowed.
THIS ACTION IS MADE FINAL. Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/ALEKSANDAR RADOSAVLJEVIC/ Examiner, Art Unit 1662
/BRENT T PAGE/Primary Examiner, Art Unit 1663