DETAILED ACTION
Notice of Pre-AIA or AIA Status
1. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Status of the Claims
2. Claims 1-10 are pending and examined.
Claim Objections
3. Claims 1, 4-6 and 9 are objected to because of the following informalities:
In claim 1, the term “HPPD” should be spelled out at its first use. The term “sequence similarity” should be amended to recite “sequence identity” to clearly reflect the fact that the percentage refers to structural identity between the sequences.
In claims 4-6 and 9, the term “being” should be replaced with a comma and the following phrase: “wherein the crop plant is,” for clarity. Appropriate correction is required.
Claim Rejections - 35 USC § 112(b)
4. 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.
5. Claims 1-10 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 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 claim 1, the recitation “wherein the fungal HPPD enzyme has less than 50% amino acid sequence similarity to an endogenous HPPD enzyme of the plant” renders the claim indefinite, for the following reasons. First, the claim does not supply a reference sequence for the endogenous HPPD enzyme, which makes it unclear relative to what the “sequence similarity” is meant to be determined. Second, the claim already requires that the “fungal HPPD enzyme” have any one of the amino acid sequences set forth in SEQ ID NO: 1, 3, or 5, which is reasonably interpreted to encompass full-length individual sequences and not a genus recited by percent identity. It is thus unclear how or whether the requirement of “50% amino acid sequence similarity” is meant to limit the HPPDs of SEQ ID NO: 1, 3, and 5 recited in the claim. Finally, the phrase “less than”, used in reference to the percent similarity, introduces further ambiguity into the claim language because it does not set the lower limit for the percent identity between the sequences, and the specification does not clarity said limit either. The metes and bounds are thus unclear.
Given that claims 2-10 depend from claim 1 and fail to recite additional limitations overcoming its indefiniteness, they are indefinite as well.
Claim 7 is indefinite for the following additional reason. The claim is directed to the crop of claim 1 comprising a nucleic acid encoding the exogenous fungal HPPD enzyme of claim 1. However, claim 1 is drawn to a plant “expressing” an exogenous fungal HPPD, which limitation necessarily requires the presence of a nucleic acid molecule encoding the enzyme. It is thus unclear how claim 7 limits the crop of claim 1.
Claim Interpretation
6. As set forth above, the claims have been found indefinite. For the purpose of the examination, the claims are given their broadest reasonable interpretation as follows. Claim 1 is read as requiring the expression of the full-length SEQ ID NO: 1, 3, or 5.
Claim 10 is drawn to a seed of the plant of claim 1, but the seed is not limited by a filial generation, and is not required to comprise the nucleic acid encoding the exogenous HPPD of SEQ ID NO: 1, 3, or 5. The claim will thus read on any wild-type seed.
Claim Rejections - 35 USC § 103
7. 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.
8. Claims 1-10 are rejected under 35 U.S.C. 103 as being unpatentable over Poree et al (US Patent Publication 2015/0159145), in view of Accinelli et al (Crop Protection (2014) 67:243-250) and GenBank Accession Number XM_024916819 (version of April 26, 2018).
Poree et al teach a plant comprising a chimeric gene encoding a Rhodococcus sp. HPPD, including wherein the chimeric gene comprises a nucleic acid sequence encoding a transit peptide, so that the chimeric gene encodes the HPPD/transit peptide fusion protein (claims 17-24). Given the evidence in paragraphs 0042, 00112, and 0122, of Poree et al, and the fact that HPPD is a chloroplast enzyme, the term “transit peptide” is reasonably interpreted as synonymous with “chloroplast transit peptide.” Poree et al disclose maize, tobacco, rice, and soybean plants, expressing said HPPD, wherein the expression conferred tolerance to the HPPD inhibitor herbicides tembotrione and isoxaflutole (Examples 5-12; see Tables 6, 7-10). Poree et al teach using chloroplast transit peptides with the HPPDs of their invention (paragraphs 0042, 0112).
Poree et al teach as follows: “Homologous nucleotide sequence may also be identified and isolated by hybridization under stringent conditions using as probes identified nucleotide sequences encoding HPPD enzymes according to the invention or parts thereof. Such parts should preferably have a nucleotide sequence comprising at least 40 consecutive nucleotides from the coding region of HPPD encoding genes sequences according to the invention, preferably from the coding region of SEQ ID No. 1, SEQ ID No. 2, SEQ ID No. 3, SEQ ID No. 15, SEQ ID No. 16 or SEQ ID No. 17. The probes may however comprise longer regions of nucleotide sequences derived from the HPPD encoding nucleic acids, such as about 50, 60, 75, 100, 200 or 500 consecutive nucleotides from any of the mentioned HPPD genes. Preferably, the probe should comprise a nucleotide sequence coding for a highly conserved region which may be identified by aligning the different HPPD proteins” (paragraph 0074).
Poree et al do not teach an HPPD enzyme comprising SEQ ID NO: 1, 3, or 5 or a nucleic acid encoding said HPPDs.
Accinelli et al teach using isolates of the fungus Trichoderma harzianum to successfully degrade bicyclopyrone (BIR), an HPPD inhibitor, resulting in less injury to soybean plants from residual bicyclopyrone in a field that had been treated with said herbicide before planting (Fig. 6 and 7; see also Abstract; Introduction on pg. 243, both col.). Accinelli et al teach that “T. harzianum was effective in reducing BIR carry over risk” (page 249, left col.).
Accinelli et al teach as follows: “Although Trichoderma has been known for a long time mainly as a biocontrol fungus, more recently its use as a plant growth promoter and for bioremediation has been considered with increasing interest … Other than being tolerant to a wide number of synthetic compounds, including pesticides, Trichoderma species produce a vast array of extracellular enzymes capable to detoxifying different xenobiotics” (page 249, left col.)
GenBank Accession Number XM_024916819 teaches the HPPD from Trichoderma harzianum that has 100% sequence identity to the instant SEQ ID NO: 1. The sequence alignment is set forth below (SEQ ID NO: 1 is the “Query”).
Score
Expect
Method
Identities
Positives
Gaps
870 bits(2248)
0.0
Compositional matrix adjust.
415/415(100%)
415/415(100%)
0/415(0%)
Query 1 MSPSAISNSPEQRPANNNGTTPDNFAIQPPADFTGYDHVTWWVGNAKQAAAYYTTLFGFE 60
MSPSAISNSPEQRPANNNGTTPDNFAIQPPADFTGYDHVTWWVGNAKQAAAYYTTLFGFE
Sbjct 1 MSPSAISNSPEQRPANNNGTTPDNFAIQPPADFTGYDHVTWWVGNAKQAAAYYTTLFGFE 60
Query 61 TTAYRGLETGSRYFASYVVCNNGVRFVFTSPLRSEAHLPEDETISDSERKLLKEIHAHLE 120
TTAYRGLETGSRYFASYVVCNNGVRFVFTSPLRSEAHLPEDETISDSERKLLKEIHAHLE
Sbjct 61 TTAYRGLETGSRYFASYVVCNNGVRFVFTSPLRSEAHLPEDETISDSERKLLKEIHAHLE 120
Query 121 RHGDAVKDVAFEVDNVEAVYNKAVAEGAIA VQGPTATKDDHGSVTTAVICTYGDTTHTLI 180
RHGDAVKDVAFEVDNVEAVYNKAVAEGAIA VQGPTATKDDHGSVTTAVICTYGDTTHTLI
Sbjct 121 RHGDAVKDVAFEVDNVEAVYNKAVAEGAIA VQGPTATKDDHGSVTTAVICTYGDTTHTLI 180
Query 181 NRRGYTGPFLPGFRAGKERTSSVEMPNVPLARIDHCVGNQSWNEMVSACAFYEQCLSFHR 240
NRRGYTGPFLPGFRAGKERTSSVEMPNVPLARIDHCVGNQSWNEMVSACAFYEQCLSFHR
Sbjct 181 NRRGYTGPFLPGFRAGKERTSSVEMPNVPLARIDHCVGNQSWNEMVSACAFYEQCLSFHR 240
Query 241 FWSVDDSQICTEFSALNSIVMASPNNLVKMPINEPAPGKKKSQIEEYVIFNSGPGVQHIA 300
FWSVDDSQICTEFSALNSIVMASPNNLVKMPINEPAPGKKKSQIEEYVIFNSGPGVQHIA
Sbjct 241 FWSVDDSQICTEFSALNSIVMASPNNLVKMPINEPAPGKKKSQIEEYVIFNSGPGVQHIA 300
Query 301 LLTPDIITSVSALRARGVEFINVPTTYYDTMRQRLKTEKRNWQLKEDLDTIQRLNILIDY 360
LLTPDIITSVSALRARGVEFINVPTTYYDTMRQRLKTEKRNWQLKEDLDTIQRLNILIDY
Sbjct 301 LLTPDIITSVSALRARGVEFINVPTTYYDTMRQRLKTEKRNWQLKEDLDTIQRLNILIDY 360
Query 361 DEAGYLLQLFTKPLMDRPTVFIEIIQRNNFEGFGAGNFKSLFEAIEREQAERGNL 415
DEAGYLLQLFTKPLMDRPTVFIEIIQRNNFEGFGAGNFKSLFEAIEREQAERGNL
Sbjct 361 DEAGYLLQLFTKPLMDRPTVFIEIIQRNNFEGFGAGNFKSLFEAIEREQAERGNL 415
GenBank Accession Number XM_024916819 also teaches a nucleic acid sequence encoding said HPPD, which has 99% identity to the instant SEQ ID NO: 2 and differs from it at two nucleotides. The sequence alignment is set forth below (SEQ ID NO: 2 is the “Query”).
Score
Expect
Identities
Gaps
Strand
2294 bits(1242)
0.0
1246/1248(99%)
0/1248(0%)
Plus/Plus
Query 1 ATGTCCCCTTCTGCTATCAGCAACTCCCCAGAGCAGCGACCTGCAAACAACAACGGCACC 60
|||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 1 ATGTCCCCGTCTGCTATCAGCAACTCCCCAGAGCAGCGACCTGCAAACAACAACGGCACC 60
Query 61 ACCCCCGACAACTTCGCTATCCAGCCTCCCGCCGACTTCACCGGCTATGACCACGTAACG 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 61 ACCCCCGACAACTTCGCTATCCAGCCTCCCGCCGACTTCACCGGCTATGACCACGTAACG 120
Query 121 TGGTGGGTTGGCAACGCCAAGCAGGCGGCCGCTTATTACACCACCCTCTTTGGGTTCGAG 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 121 TGGTGGGTTGGCAACGCCAAGCAGGCGGCCGCTTATTACACCACCCTCTTTGGGTTCGAG 180
Query 181 ACTACGGCCTATCGTGGACTCGAGACTGGAAGCCGATACTTCGCTTCCTATGTCGTCTGC 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 181 ACTACGGCCTATCGTGGACTCGAGACTGGAAGCCGATACTTCGCTTCCTATGTCGTCTGC 240
Query 241 AACAATGGCGTCCGCTTCGTCTTCACGTCGCCTCTGCGATCGGAGGCTCACCTCCCTGAA 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 241 AACAATGGCGTCCGCTTCGTCTTCACGTCGCCTCTGCGATCGGAGGCTCACCTCCCTGAA 300
Query 301 GATGAGACCATCTCTGATTCTGAGCGGAAGCTCCTGAAGGAGATTCACGCTCACCTCGAG 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 301 GATGAGACCATCTCTGATTCTGAGCGGAAGCTCCTGAAGGAGATTCACGCTCACCTCGAG 360
Query 361 AGACACGGCGATGCCGTCAAGGACGTTGCCTTTGAAGTTGACAACGTCGAGGCCGTATAC 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 361 AGACACGGCGATGCCGTCAAGGACGTTGCCTTTGAAGTTGACAACGTCGAGGCCGTATAC 420
Query 421 AACAAGGCCGTGGCTGAGGGCGCCATCGCCGTCCAAGGCCCAACCGCCACCAAGGATGAT 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 421 AACAAGGCCGTGGCTGAGGGCGCCATCGCCGTCCAAGGCCCAACCGCCACCAAGGATGAT 480
Query 481 CACGGCTCCGTCACCACGGCCGTCATCTGCACCTATGGCGATACCACCCACACTCTCATC 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 481 CACGGCTCCGTCACCACGGCCGTCATCTGCACCTATGGCGATACCACCCACACTCTCATC 540
Query 541 AACCGCCGGGGCTACACGGGACCTTTCCTGCCCGGCTTCCGCGCCGGCAAGGAGCGCACC 600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 541 AACCGCCGGGGCTACACGGGACCTTTCCTGCCCGGCTTCCGCGCCGGCAAGGAGCGCACC 600
Query 601 TCGTCCGTGGAGATGCCCAACGTGCCCCTTGCCCGCATCGACCACTGCGTCGGCAACCAG 660
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 601 TCGTCCGTGGAGATGCCCAACGTGCCCCTTGCCCGCATCGACCACTGCGTCGGCAACCAG 660
Query 661 TCGTGGAACGAAATGGTCTCGGCCTGCGCCTTTTACGAGCAGTGCCTGTCCTTCCACCGT 720
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 661 TCGTGGAACGAAATGGTCTCGGCCTGCGCCTTTTACGAGCAGTGCCTGTCCTTCCACCGT 720
Query 721 TTCTGGTCCGTCGACGACTCCCAGATCTGCACCGAGTTCTCGGCCCTCAACTCCATCGTC 780
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 721 TTCTGGTCCGTCGACGACTCCCAGATCTGCACCGAGTTCTCGGCCCTCAACTCCATCGTC 780
Query 781 ATGGCCTCGCCCAACAACCTCGTCAAGATGCCCATCAACGAGCCCGCCCCGGGCAAGAAG 840
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 781 ATGGCCTCGCCCAACAACCTCGTCAAGATGCCCATCAACGAGCCCGCCCCGGGCAAGAAG 840
Query 841 AAGTCCCAGATCGAGGAGTACGTCATCTTCAACTCCGGCCCGGGCGTCCAGCACATCGCC 900
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 841 AAGTCCCAGATCGAGGAGTACGTCATCTTCAACTCCGGCCCGGGCGTCCAGCACATCGCC 900
Query 901 CTCCTCACCCCGGACATCATCACCTCCGTCTCGGCCCTCCGCGCCCGCGGCGTCGAGTTC 960
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 901 CTCCTCACCCCGGACATCATCACCTCCGTCTCGGCCCTCCGCGCCCGCGGCGTCGAGTTC 960
Query 961 ATCAACGTGCCCACCACTTACTACGACACCATGCGCCAGCGCCTCAAGACGGAGAAGCGC 1020
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 961 ATCAACGTGCCCACCACTTACTACGACACCATGCGCCAGCGCCTCAAGACGGAGAAGCGC 1020
Query 1021 AACTGGCAGCTCAAGGAGGACCTGGACACCATCCAGCGCCTCAACATCCTCATCGACTAC 1080
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 1021 AACTGGCAGCTCAAGGAGGACCTGGACACCATCCAGCGCCTCAACATCCTCATCGACTAC 1080
Query 1081 GACGAGGCCGGCTACCTCCTGCAGCTCTTCACCAAGCCGCTCATGGACCGCCCTACCGTC 1140
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 1081 GACGAGGCCGGCTACCTCCTGCAGCTCTTCACCAAGCCGCTCATGGACCGCCCTACCGTC 1140
Query 1141 TTCATTGAGATTATCCAGAGAAACAACTTTGAGGGCTTCGGCGCCGGCAACTTCAAGAGC 1200
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 1141 TTCATTGAGATTATCCAGAGAAACAACTTTGAGGGCTTCGGCGCCGGCAACTTCAAGAGC 1200
Query 1201 TTGTTCGAGGCCATTGAGCGCGAGCAGGCCGAGCGAGGAAACTTGTAA 1248
|||||||||||||||||||||||||||||||||||||||||| |||||
Sbjct 1201 TTGTTCGAGGCCATTGAGCGCGAGCAGGCCGAGCGAGGAAACCTGTAA 1248
At the time of filing, it would have been prima facie obvious to modify the teachings of Poree et al, using the teachings of Accinelli et al and GenBank Accession Number XM_024916819, and obtain an expression construct encoding the HPPD of the GenBank Accession Number XM_024916819, including wherein the HPPD is fused to a chloroplast transit peptide.
Given the conserved nature of a number of known HPPD domains, as taught by Poree et al, one would have been able to predictably identify the protein of GenBank Accession Number XM_024916819 as an HPPD, as well as to isolate its coding sequence. Moreover, one would have recognized that the amino acid sequence would have made obvious at least one nucleic acid sequence encoding it, due to the properties of the genetic code.
It would have been obvious to exogenously express said construct in any crop plant, including any monocot or dicot crop such as corn or soybean, as taught by Poree et al. It would have been obvious to use, in said expression construct, the nucleic acid of GenBank Accession Number XM_024916819, which would be considered an obvious variant of the instant SEQ ID NO: 2, given that both encode the same protein.
One would have been motivated to combine said teachings, and to specifically select the HPPD from Trichoderma harzianum given the teachings of Accinelli et al regarding the ability of said fungus to inactivate bicyclopyrone, an HPPD inhibitor. One would have also been motivated to arrive at the claimed invention given the desirability of obtaining HPPD inhibitor tolerant plants, as illustrated by the teachings of Poree et al.
Given the teachings of Accinelli et al, the fact that the HPPD T. harzianum was known in the prior art, and in view of the routine nature of the molecular biology methods involved, one would have had reasonable expectation of success in arriving at the claimed plant, including wherein the plant is tolerant to at least one HPPD inhibitor.
Claim Rejections - 35 USC § 102
9. 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.
10. Claim 10 is rejected under 35 U.S.C. 102(a)(1) as being anticipated by Poree et al (US Patent Publication 2015/0159145).
The claim is drawn to a seed of the plant of claim 1, wherein the seed is not limited by a filial generation and is not required to comprise the nucleic acid encoding the fungal HPPDs of SEQ ID NO: 1, 3, or 5. The claim will thus read on any seed.
The teachings of Poree et al are set forth above. In addition, Poree et al teach seeds, including those of tobacco (Example 4). In view of the above claim interpretation, any seed of Poree et al will read and anticipate the limitations of claim 10.
Relevant Prior Art
11. While the following art was not cited in the above rejections, it is made of record as it is relevant to the claimed subject matter.
Choudhury et al, Biodegradation of topramezone by a Trichoderma isolate in soil, Weeds -Journal of Asian-Pacific Weed Science Society (2019) 1:43-54, published August 2019. Choudhury et al teach that Trichoderma isolates degraded 85% of topramezone without 30 days of incubation, which is much faster than the reported half-life of the herbicide (Abstract).
Conclusion
12. No claims are allowed.
13. Any inquiry concerning this communication or earlier communications from the examiner should be directed to MYKOLA V KOVALENKO whose telephone number is (571)272-6921. The examiner can normally be reached Mon.-Fri. 9:00-5:30 PST.
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/MYKOLA V. KOVALENKO/Primary Examiner, Art Unit 1662
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