DETAILED ACTION
Applicant’s election without traverse of the species SEQ ID NO:1 in the reply filed on 24 February 2026 is acknowledged.
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claim Rejections - 35 USC § 101
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.
Claims 1-2 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a natural phenomenon without significantly more. This judicial exception is not integrated into a practical application. The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception.
Claim 1 encompasses SEQ ID NO:1, which is the naturally-occurring chloroplast psaJ promoter from Arabidopsis thaliana (Table 2). The claim recites no additional element. Thus, this claim is not directed to significantly more than a product of nature.
Claim 2 recites the additional element of a transformation vector comprising the promoter. However, “vector” does not confer any structure, as it encompasses the Arabidopsis chloroplast genome that the promoter is located on. “[T]ransformation” also does not confer any structure, as any DNA can be used for transformation. Thus, this claim is not directed to significantly more than a product of nature.
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 1-6 are 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 a promoter of SEQ ID NO:1, does not reasonably provide enablement for the full scope of organellar promoters with 90% identity to SEQ ID NO:1 or with any number of nucleotide substitutions, insertions or deletions in SEQ ID NO:1. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make the invention commensurate in scope with these claims.
The claims are broadly drawn to an organellar promoter with 90% identity to SEQ ID NO:1 or with deletions, substitutions or additions of one or more bases in SEQ ID NO:1 or with 90% identity to a promoter with deletions, substitutions or additions of one or more bases in SEQ ID NO:1.
A. The full scope of organellar promoters with 90% identity to SEQ ID NO:1 or with 90% identity to a promoter with deletions, substitutions or additions of one or more bases in SEQ ID NO:1 are not enabled
Nucleic acids with 90% identity to the 229-nucleotide long SEQ ID NO:1 would have 22 nucleotide substitutions relative to SEQ ID NO:1. Nucleic acids with 90% identity to a promoter with deletions, substitutions or additions of one or more bases in SEQ ID NO:1 encompass those with any number of nucleotide substitutions relative to SEQ ID NO:1.
The instant specification fails to provide guidance for how to make organellar promoters with 90% identity to SEQ ID NO:1 or with 90% identity to a promoter with deletions, substitutions or additions of one or more bases in SEQ ID NO:1.
The specification provides no guidance whatsoever for making nucleotide substitutions in SEQ ID NO:1 and still producing an organellar promoter.
SEQ ID NO:1 is an Arabidopsis thaliana chloroplast psaJ promoter:
KX551970
LOCUS KX551970 154515 bp DNA circular PLN 02-AUG-2016
DEFINITION Arabidopsis thaliana chloroplast, complete genome.
ACCESSION KX551970
VERSION KX551970.1
KEYWORDS .
SOURCE chloroplast Arabidopsis thaliana (thale cress)
ORGANISM Arabidopsis thaliana
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae;
Pentapetalae; rosids; malvids; Brassicales; Brassicaceae;
Camelineae; Arabidopsis.
REFERENCE 1 (bases 1 to 154515)
AUTHORS Stadermann,K.B., Holtgraewe,D. and Weisshaar,B.
TITLE The chloroplast genome sequence of Arabidopsis thaliana Landsberg
erecta assembled from SMRT sequencing data
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 154515)
AUTHORS Stadermann,K.B., Holtgraewe,D. and Weisshaar,B.
TITLE Direct Submission
JOURNAL Submitted (13-JUL-2016) Chair of Genome Research, Bielefeld
University, Universitaetsstrasse 25, Bielefeld, NRW 33615, Germany
COMMENT ##Assembly-Data-START##
Assembly Method :: sprai v. 0.9.9.7
Sequencing Technology :: PacBio
##Assembly-Data-END##
FEATURES Location/Qualifiers
gene complement(66534..66607)
/gene="trnP-TGG"
tRNA complement(66534..66607)
/gene="trnP-TGG"
/product="tRNA-Pro"
gene 66969..67103
/gene="psaJ"
CDS 66969..67103
/gene="psaJ"
/codon_start=1
/transl_table=11
/product="photosystem I subunit IX"
/protein_id="ANW47810.1"
/translation="MRDLKTYLSVAPVLSTLWFGSLAGLLIEINRLFPDALTFPFFSF"
Query Match 100.0%; Score 229; Length 154515;
Best Local Similarity 100.0%;
Matches 229; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 GGCCTTTACGTTTTCAAATGGAATCGATAAGATCGTTCTAGTCGACAATATTAAAATTCT 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 66779 GGCCTTTACGTTTTCAAATGGAATCGATAAGATCGTTCTAGTCGACAATATTAAAATTCT 66838
Qy 61 AATTTTGAAAGCGGGGGGACGGAAGTTACATATACAAATACAAGAACTTCTTAATTACAT 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 66839 AATTTTGAAAGCGGGGGGACGGAAGTTACATATACAAATACAAGAACTTCTTAATTACAT 66898
Qy 121 GTACATCTGTAATTATATATATTACTATATATAATGTAATACAATAAAGAAGAAAGAAGG 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 66899 GTACATCTGTAATTATATATATTACTATATATAATGTAATACAATAAAGAAGAAAGAAGG 66958
Qy 181 AGGATTTCTAATGCGAGATCTAAAAACATATCTTTCCGTAGCACCGGTA 229
|||||||||||||||||||||||||||||||||||||||||||||||||
Db 66959 AGGATTTCTAATGCGAGATCTAAAAACATATCTTTCCGTAGCACCGGTA 67007
The sequence includes part of the open reading frame, starting at nucleotide 191, corresponding to nucleotide 66969 of Stadermann et al (2016, GenBank Accession No. KX551970, https:// www.ncbi.nlm.nih.gov/ nuccore/KX551970). It also includes the 37 nucleotide-long 5’ UTR (Nagashima et al, 2014, Biosci. Biotechnol. Biochem. 68:694-704; Fig. 4), which starts at nucleotide 153:
ggcctttacg ttttcaaatg gaatcgataa gatcgttcta gtcgacaata ttaaaattct 60
aattttgaaa gcggggggac ggaagttaca tatacaaata caagaacttc ttaattacat 120
gtacatctgt aattatatat attactatat ata atgtaat acaataaaga agaaagaagg 180
▲-37
aggatttcta atgcgagatc taaaaacata tctttccgta gcaccggta
▲ ORF start
Unlike most chloroplast promoters, which are recognized by a nuclear-encoded RNA polymerase (NEP), the Arabidopsis psaJ promoter is recognized by a plastid encoded RNA polymerase (PEP) (Nagashima et al, pg 697, left column; pg 700, left column, ¶1, to right column, ¶1). The sequence elements responsible for the interaction of the psaJ promoter and the PEP transcription factors are not known (pg 700, right column, ¶1).
The instant specification fails to provide guidance for which nucleotides of SEQ ID NO:1 can be altered and to which other nucleotides, and which nucleotides must not be changed, to maintain PEP promoter activity of the nucleic acid. The specification also fails to provide guidance for which nucleotides can be deleted and which regions of the promoter can tolerate insertions and still function as a PEP promoter.
As the specification does not provide guidance for modifying SEQ ID NO:1, undue trial and error experimentation would be required to screen through the myriad of nucleic acids encompassed by the claims to identify those with organellar promoter activity, if such nucleic acids are even obtainable.
B. Mitochondrial and plastid transformation are not enabled over the full scope of organisms
Claim 3 is drawn to a cell of any species whose organelle is transformed with a vector comprising an organellar promoter with 90% identity to SEQ ID NO:1 or with 90% identity to a promoter with deletions, substitutions or additions of one or more bases in SEQ ID NO:1. Claim 4 specifies that the organelle is a plastid or mitochondria, which are the only organelles with DNA.
The specification does not provide guidance for how to transform the chloroplasts of the full scope of plant species.
Even though plastid transformation was first developed 30 years prior to the filing of the instant application, it has only been successful in a very few plant species and in no monocots (Bock, 2015, Annual Review of Plant Biology 66:211-241, see pg 221, $4; Table 2; Maliga, 2022, Nature Plants 8:996-1006, see pg 996, right column, T2, to pg 997, left column, I, Table 1). Plastid transformation is not possible even in many plant species where nuclear transformation is well-established (Jakubiec et al, 2021, Nature Plants 7:932-941, see pg 937, right column, 4). The specification does not teach how to transform the plastids of the full scope of monocots and dicots.
Plastid transformation is only enabled in two (Physcomitrella patens and Marchantia polymorpha) of the approximately 12,000 moss species and one (Chlamydomonas reinhardtii) of the approximately 100,000 algal species. The specification does not teach how to transform the plastids of the full scope of moss and algal species.
The specification does not provide guidance for how to transform the mitochondria of the full scope of organisms.
Even 6 years after the filing of the instant priority document, mitochondrial transformation in plants is not possible (Forner, 2025, Plant Physiol. 198, kiaf197, https://doi.org/10.1093/plphys/kiaf197; see pg 4, box 2; pg 9, left column, ¶3, and the paragraph spanning the columns on pg 9). Mitochondrial transformation has only been achieved in a single-cell yeast species and a single-cell algal species (pg 9, Outstanding questions box).
It is not possible in other fungi or algae or in plants, animals, or other organisms, as encompassed by the claims.
Further, even if plastid and mitochondrial transformation were enabled over the full scope of organisms, it is unlikely that an organellar promoter with 90% identity to SEQ ID NO:1 or with 90% identity to a promoter with deletions, substitutions or additions of one or more bases in SEQ ID NO:1 would function in the plastids and mitochondria of the full scope of organisms. Transcription from the Arabidopsis psaJ promoter of SEQ ID NO:1 is achieved via an Arabidopsis plastid encoded RNA polymerase (PEP) and a particular transcription factor, Sig2 (Nagashima et al, pg 697, left column; pg 700, left column, paragraph 1, to right column, paragraph 1). In entire plant clades, PEP-promoters differ considerably from those in organisms like Arabidopsis (Lyubetsky et al, Biology Direct 2010, 5:34; see paragraph spanning the columns on pg 7). It is highly unlikely that RNA polymerases and transcription factors that recognize the Arabidopsis psaJ promoter of SEQ ID NO:1 are present in the full scope of plastids and mitochondria.
The specification fails to overcome the unpredictability in the art of plastid and mitochondrial transformation as it provides no working examples of the full scope of plastids or mitochondria transformed with a vector comprising an organellar promoter with 90% identity to SEQ ID NO:1 or with 90% identity to a promoter with deletions, substitutions or additions of one or more bases in SEQ ID NO:1.
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.
Claims 1-6 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 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 pre-AIA the inventor(s), at the time the application was filed, had possession of the claimed invention.
The claims require organellar promoters with 90% identity to SEQ ID NO:1 or with 90% identity to a promoter with deletions, substitutions or additions of one or more bases in SEQ ID NO:1.
Nucleic acids with 90% identity to the 229-nucleotide long SEQ ID NO:1 would have 22 nucleotide substitutions relative to SEQ ID NO:1. Nucleic acids with 90% identity to a promoter with deletions, substitutions or additions of one or more bases in SEQ ID NO:1 encompass those with any number of nucleotide substitutions relative to SEQ ID NO:1.
As detailed in the enablement rejection and incorporated herein, SEQ ID NO:1 is an Arabidopsis thaliana chloroplast psaJ promoter. SEQ ID NO:1 includes part of the open reading frame, the 37 nucleotide-long 5’ UTR, as well of the psaJ promoter.
The Arabidopsis psaJ promoter interacts with the SIG2 transcriptional regulator (Nagashima et al, 2004, Biosci. Biotechnol. Biochem. 68:694-704, see pg 700, left column, ¶2), but the sequence elements required for this interaction are not known (pg 700, right column, ¶1).
The structural features that distinguish organellar promoters with 90% identity to SEQ ID NO:1 from other nucleic acids with 90% identity to SEQ ID NO:1 are not described in the specification. The structural features that distinguish organellar promoters with 90% identity to a promoter with deletions, substitutions or additions of one or more bases in SEQ ID NO:1 from other nucleic acids with 90% identity to a promoter with deletions, substitutions or additions of one or more bases in SEQ ID NO:1 are not described in the specification.
The specification does not describe any motifs that are necessary and sufficient structural elements of an organellar promoter.
The only species described in the specification is SEQ ID NO:1.
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.
Hence, Applicant has not, in fact, described organellar promoters with 90% identity to SEQ ID NO:1 or with 90% identity to a promoter with deletions, substitutions or additions of one or more bases in SEQ ID NO:1 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 2-6 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 2 lacks antecedent basis for the limitation “the sequence in claim 1” as “sequence” is recited in claim 1 in 4 different places, in line 2, and in each of (a), (b), and (c). It is not clear to which the recitation refers.
Claim 6 is indefinite in its recitation of “plant body” as plants do not have bodies.
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale or otherwise available to the public before the effective filing date of the claimed invention.
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 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.
Claims 1-2 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Stadermann et al (2016, GenBank Accession No. KX551970, https:// www.ncbi.nlm.nih.gov/ nuccore/KX551970).
Stadermann et al teach the sequence of the Arabidopsis chloroplast genome. Bases 66779-67007 have 100% identity to the instant SEQ ID NO:1. See the alignment in the enablement rejection above; that alignment is incorporated herein.
As “transformation vector” confers no structure, as any DNA can be used for transformation, the chloroplast genome comprising this sequence reads on the instant claim 2.
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.
Claims 1-6 are rejected under 35 U.S.C. 103(a) as being unpatentable over Yu et al (2017, Plant Physiol. 175:186-193) in view of Daniell (US 2010/0325756), Stadermann et al (2016, GenBank Accession No. KX551970, https:// www.ncbi.nlm.nih.gov/ nuccore/KX551970), and Nagashima et al (2004, Biosci. Biotechnol. Biochem. 68:694-704).
The claims are drawn to the Arabidopsis psaJ promoter, a transformation vector comprising it, and plant cells and plants whose plastids are transformed with the vector.
Yu et al teach a method of transforming Arabidopsis plastids with a vector comprising a construct comprising flanking sequences that target an operon comprising the tobacco Prrn promoter operably linked to two different selectable markers to region upstream of the trnV gene (pg 192, left column, ¶6; pg 187, right column, ¶2; Fig. 2). The transformation frequency was increased when the vector was transformed into an acc2 null mutant Arabidopsis line, which makes untransformed cells sensitive to spectinomycin (pg 190, left column, ¶2-3).
Yu et al do not teach use of the Arabidopsis psaJ promoter in the vector used to transform Arabidopsis plastids.
Daniell teaches that the intergenic region upstream of the psbA coding sequence of chloroplast genomes from a wide range of plants has much less similarity across taxa than do the psbA coding sequences in these plants (¶45) and that these sequence differences meant that psbA UTRs of these plants had different structures (¶46). The practical effect of this was seen when the plastids of tobacco and lettuce were each transformed with constructs comprising the lettuce and tobacco psbA promoters and UTRs operably linked to a DNA encoding a non-plastid protein (¶47). Lower expression of the protein was seen in lettuce transformed with the construct comprising the tobacco promoter and UTR than in lettuce transformed with the construct comprising the lettuce promoter, and lower expression of the protein was seen in tobacco transformed with the construct comprising the lettuce promoter and UTR than in tobacco transformed with the construct comprising the tobacco promoter (¶49-55).
The teachings of Stadermann et al are discussed above, with the alignment to SEQ ID NO:1 shown enablement rejection above and incorporated herein. The sequence includes the Arabidopsis psaJ promoter.
Nagashima et al teach that the transcription start site for the psaJ open reading frame is 37 nucleotides upstream of the starting methionine (pg 700, left column, ¶2). Unlike most chloroplast promoters, which are recognized by a nuclear-encoded RNA polymerase (NEP), the Arabidopsis psaJ promoter is recognized by a plastid encoded RNA polymerase (PEP) (Nagashima et al, pg 697, left column; pg 700, left column, ¶1, to right column, ¶1).
Before the effective filing date of the claimed invention, it would have been obvious to one of ordinary skill in the art to modify Yu et al’s method of transforming Arabidopsis plastids to use the Arabidopsis psaJ promoter in the transformation vector. One of ordinary skill in the art would have been motivated to do so because use of regulatory sequences endogenous to the plant being transformed because Daniell recommends use of species specific (endogenous) regulatory sequences when transforming the plastids of a plant (¶66). The Arabidopsis psaJ regulatory sequence is one Arabidopsis plastid regulatory sequence for use in Arabidopsis plastid transformation.
One of ordinary skill in the art would have included the Arabidopsis psaJ 5’ UTR in the regulatory sequence because of its role in increasing expression of the protein whose coding sequence is operably linked to the promoter (Daniell, ¶49-55). The Arabidopsis psaJ 5’ UTR is the 37 nucleotides immediately upstream from the start codon- (Nagashima et al, Fig. 4).
Conclusion
No claim is allowed.
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/Anne Kubelik/Primary Examiner, Art Unit 1663
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