T 1499/09 (Xylosyltransferase/GLÖSSL) 23-10-2012

I. The appeal lies from the decision of the opposition division posted on 30 March 2009 revoking the European patent No. 1 263 968 with the title "Beta 1,2-xylosyl transferase-gene from Arabidopsis" under Article 101(3)(b) EPC. The patent at issue is based on European patent application No. 01919367.1 which was filed as international application under the PCT and published as WO 01/64901 (in the following "the application as filed"). The patent was granted with 20 claims.

II. The opposition to the grant of the patent was based on the grounds for opposition mentioned in Article 100(a), (b) and (c) EPC, in particular that the claimed subject-matter lacked novelty (Article 54 EPC), inventive step (Article 56 EPC) and industrial application (Article 57 EPC), that the granted claims encompassed subject-matter which went beyond the content of the application as filed, and that the claimed invention was not disclosed in a manner sufficiently clear and complete for a person skilled in the art to carry it out.

III. In the decision under appeal, the opposition division found that Article 100(c) EPC prejudiced the maintenance of the patent as granted (main request), that the amendments introduced into the claims of the first auxiliary request then on file contravened Article 123(3) EPC, and that the subject-matter of the claims according to the second and third auxiliary requests then on file lacked novelty and inventive step, respectively.

IV. Together with the statement of grounds of appeal, the patent proprietor (appellant) submitted additional evidence and four sets of claims as first to fourth auxiliary requests replacing the previous auxiliary requests. Maintenance of the patent as granted remained his main request. As a subsidiary request, oral proceedings were requested.

V. The opponent (respondent) submitted observations on the statement of grounds of appeal and requested oral proceedings.

VI. The appellant replied and put forward additional arguments.

VII. The parties were summoned to oral proceedings. In a communication under Article 15(1) of the Rules of Procedure of the Boards of Appeal (RPBA) attached to the summons to oral proceedings, the board expressed its provisional opinion on some of the issues to be discussed, in particular issues in connection with Articles 123(2), 54 and 56 EPC. In view of the new evidence and requests filed by the appellant in appeal proceedings, the board drew attention to Article 12(4) RPBA.

VIII. In response to the board's communication, the appellant submitted a further amended set of claims as new auxiliary request 1b.

IX. By letter of 27 September 2012, the respondent withdrew its request for oral proceedings and informed the board that it would not be attending the scheduled oral proceedings.

X. During the oral proceedings held on 23 October 2012, in which the respondent was not represented, the appellant filed amended claims 1 to 17 as his new main request.

XI. Amended claims 1, 10 and 11 of the new main request read:

"1. An isolated DNA molecule characterised in that it codes for a plant protein having beta1,2—xylosyl transferase activity and in that it comprises a sequence selected from the group consisting of

• a sequence SEQ ID NO 8 with an open reading frame from base pair 227 to base pair 1831,

• a sequence which is at least 70% identical with SEQ ID NO: 8,

• a sequence which is complementary to SEQ ID NO: 8;

with the proviso that a DNA sequence as disclosed in EP 1 033 405 A2 under SEQ ID NO 77276 translated to an amino acid sequence according to SEQ ID NO 77277 of EP 1 033 405 A2 is excepted.

10. A method of preparing recombinant host cells, particularly plant cells, or plants, wherein the production of beta1,2—xylosyltransferase is suppressed or completely stopped, characterised in that the vector according to claim 7 is inserted into said host cell or plant, respectively.

11. A method of preparing recombinant host cells, particularly plant cells or plants, respectively, characterised in that the DNA molecule according to any one of claims 1 to 5 with a deletion, insertion and/or substitution mutation is inserted into the genome of said host cell or plant, respectively, at the position of the non—mutated, homologous sequence, wherein the production of beta1,2-xylosyltransferase is suppressed or completely stopped."

Dependent claims 2 and 3, which are derived from claim 3 as granted, and dependent claims 4 and 5, which are identical to the corresponding claims of the patent as granted, relate to particular embodiments of the DNA molecule according to claim 1. Independent claims 6 and 7 relate to biologically functional vectors and are identical to claims 8 and 9 of the patent as granted. Independent claims 8 and 9, which are identical to claims 11 and 12 of the patent as granted, concern a method of preparing a cDNA and a method of cloning a betal,2-xylosyltransferase, respectively. Claim 12, which has been amended to adapt the reference to the numbering of the previous claims, is directed to recombinant plants or plant cells prepared by a method according to claims 10 or 11. Claims 13 to 17 are identical to claims 16 to 20 of the patent as granted, except for the references being adapted to the new numbering. Claims 6, 7 and 10 of the patent as granted have been deleted.

XII. The following documents are referred to in the present decision:

(1): WO 99/29835, published on 17 June 1999;

(2): EMBL databank, Accession No. AB015479, created on 19 June 1998;

(8): S. Pagny et al., 2003, The Plant Journal, Vol. 33, pages 189 to 203;

(9): P. Bencúr et al., 2005, Biochem. J., Vol. 388, pages 515 to 525;

(11): H. Puchta, 2002, Plant Molecular Biology, Vol. 48, pages 173 to 182;

(12): T. Mengiste and J. Paszkowski, July/August 1999, Biol. Chem., Vol. 380, pages 749 to 758;

(13): R. Terada et al., October 2002, nature biotechnology, Vol. 20, pages 1030 to 1034;

(16): R. Strasser et al., 2000, FEBS Letters, Vol. 472, pages 105 to 108;

Annex 1: Results of a search of nucleic acid sequence libraries available prior to 3 March 2000 using the partial cDNAs described in document (1) (SEQ ID NOs: 6 and 7);

Annex 5: Nucleotide alignment of SEQ ID NOs: 6 and 7 of document (1) with SEQ ID NO: 8 of the patent;

Annex VII: S. A. Kempin et al., 23 October 1997, Nature, Vol. 389, pages 802 and 803;

Annex VIII: M. Hanin et al., 2001, The Plant Journal, Vol. 28, No. 6, pages 671 to 677.

XIII. The submissions made by the appellant may be summarized as follows:

Admission of the new main request into the proceedings

The new set of amended claims did not give rise to additional issues, but overcame objections under Article 123(2) EPC on which the board had expressed an adverse provisional opinion. The amendments were straightforward and did not require further discussion.

Article 123(2) EPC

Amended claim 1 had a basis in claims 1, 2 and 3 of the application as filed. Replacing the wording "above sequence" in the original claim 1 by "SEQ ID NO: 8" did not introduce subject-matter extending beyond the content of the application as filed. It was absolutely clear to the skilled person reading the application as filed that "homology" in the context of a quantitative measure meant "identity".

Claim 11 had a basis in original claim 14. The reference to the omitted claim 6 was replaced by the features of this claim. The additional feature "wherein the production of beta1,2-xylosyltransferase is suppressed or completely stopped" had a basis in claim 15 of the application as filed.

Article 123(3) EPC

The wording "(sequence A)", which had been introduced into claim 1 as granted to define different sequence variants (50% identical, hybridizing sequence, genetic code degenerated sequence), served only as a place holder for the phrase "SEQ ID NO: 8 with an open reading frame from base pair 227 to base pair 1831". Thus, deleting this wording or replacing it by "SEQ ID NO: 8" did not extend the scope of protection conferred by the patent as granted.

Article 83 EPC

It was possible for a skilled person to modify the SEQ ID NO: 8 to obtain a sequence which still encoded active betal,2-xylosyltransferase. The activity could be tested in an assay as described in the application.

The insertion of a given sequence into a plant genome, in particular by homologous recombination was well understood at the priority date and described in the application. Even though the application provided only a reference to a method for gene targeting in the moss Physcomitrella patens (see page 16, third full paragraph, lines 5 and 6 of the application), the same method could be applied to the transformation of other plants. Annexes VII and VIII showed successful gene targeting methods in Arabidopsis. Low transformation frequency in higher plants was not a serious obstacle because successful recombination events could be screened as described in the application. Thus, the requirements of Article 83 EPC were met.

Article 54 EPC

The subject-matter of claim 1 was novel over document (2). This document was not prior "art" because it did not contain a technical teaching with regard to the enzymatic activity. Since the document did not provide an enabling disclosure, a DNA molecule encoding a xylosyltransferase was not made available to the public.

Article 56 EPC

Document (1) represented the closest state of the art. The invention claimed in the patent differed from the teachings in document (1) in that the patent provided a full-length sequence encoding an active xylosyl transferase whereas document (1) did not. Moreover, while document (1) related to a soybean xylosyl transferase, the patent provided a sequence that encoded an Arabidopsis thaliana xylosyltransferase.

The objective technical problem was the provision of a full-length nucleotide sequence that encoded an active plant betal,2-xylosyltransferase. A person skilled in the art could have tried to obtain the full-length sequence coding for the soybean xylosyltransferase by using the partial sequence provided in Figure 10 of document (1) to clone the xylosyltransferase gene from a soybean library. However, there was no evidence on file that this approach would have been successful, nor that the skilled person would have arrived at a sequence which fell under the scope of claim 1.

The opposition division's assumption that the skilled person would have relaunched a BLAST search was speculative. The skilled person could possibly have done so, but it was a completely unproven allegation without any support in document (1) that this would have been obvious. Moreover, it had not been proven that the skilled person could have found document (2) in a BLAST search. Even though this document was in principle available at the priority date, the authors of document (1) had not been able to find any homologous sequences in a BLAST search (see statements on page 6, lines 19 and 20 of document (1)).

Document (1) did not describe a single xylosyl transferase protein, but two different soybean proteins which were not related to each other (see page 23, lines 1 to 3). Although the sequence of three peptides from the 56 kDa protein and two peptides from the 59 kDa protein was provided, document (1) did not describe any primers based on the peptide sequences, nor did it provide any incentive to try to use such primers in an amplification reaction with Arabidopsis mRNA instead of soybean mRNA. In any case, it had not been proven that such amplification reactions would have identified the claimed DNA molecule.

The results of the search presented in Annex 1 did not represent what the skilled person would have found at the priority date because sequence database entries created or modified after that date were retrieved. Thus, Annex 1 was artificial and without any probative value. Nor could the examples of the patent itself serve as evidence of what the skilled person would have retrieved from a BLAST search. The search that led to the isolation of the Arabidopsis xylosyltransferase gene had been done using a combination of one peptide of the 56 kDa protein and a truncated version of a peptide of the 59 kDa protein. The skilled person would not have taken this course of action which deviated from the routine practice.

Moreover, retrieving a hit in a BLAST search was not sufficient to provide the present invention. Generating a true cDNA sequence from an unannotated genomic clone was far from trivial. In silico methods did not recognise reliably the correct start and stop codons. Without the knowledge of the correct gene structure, the skilled person would have encountered difficulties designing amplification primers to obtain the xylosyl transferase cDNA.

Starting from the cDNA sequences provided in document (1) (SEQ ID NOs: 6 and 7) the skilled person had no reasonable expectation of success. Since all three reading frames of SEQ ID NO: 6 contained stop codons, the skilled person would not have expected this sequence to encode a xylosyltransferase protein. Thus, inventive step should be acknowledged.

XIV. The submissions by the respondent in writing were essentially as follows (N.B. The respondent did not attend the oral proceedings during which the new main request was filed. Thus, the objections made in writing to corresponding subject-matter of the previous requests are reported hereinafter):

Article 123(2) EPC

The decision under appeal was deficient because the opposition division failed to reach a formal decision on each of the objections raised under Article 123(2) EPC.

Each of claims 1 and 3 as originally filed claimed sequences of a numerical percentage homology with SEQ ID NO: 8. There was no basis in the application as filed for sequences being percentage identical to the reference sequence. Since "identity" and "homology" neither had the same meaning nor were calculated or estimated by the same methods, there was a reasonable doubt that the amendment of the claims to read "identical" altered the meaning or scope of the original claims and, consequently offended against Article 123(2) EPC.

Moreover, the addition of the wording "... selected from the group consisting of ..." to claim 1 restructured the original claim 1 so that the range of sequences which the reference DNA molecule is "comprised of" was broadened. DNA molecules which comprised a sequence at least 70% identical with SEQ ID NO: 8 were not encompassed by the original claim 1.

Articles 84 and 123(3) EPC

Claim 11, which was directed to a method of preparing recombinant host cells, had been amended to refer back to the DNA molecule of any of claims 1 to 5 with the additional requirement of a deletion, insertion and/or substitution mutation. Contrary to the requirement in claims 1 to 5, less than full length sequences not encoding betal,2-xylosyltransferase activity could be used in the claimed method. Because of uncertainty over the requirement for encoding a protein with xylosyl transferase activity, the claim lacked clarity within the meaning of Article 84 EPC and it could be reasonably assumed that the amendment resulted in a broadening of the scope of protection conferred by the patent, contrary to Article 123(3) EPC.

Article 83 EPC

Claim 1 and claims dependent or referring to claim 1 lacked enablement contrary to Article 83 EPC. The specification as originally filed did not identify or describe the essential elements of the amino acid or nucleotide sequences of the betal,2-xylosyltransferase that were responsible for the xylosyltransferase activity. The average skilled person was therefore left in the dark as to the nature and extent of the changes that could be made to the SEQ ID NO: 8 whilst preserving the enzyme activity.

While document (8) provided some guidance as to where deletions could be made in the N-terminal region of the betal,2-xylosyltransferase, neither this document nor document (9) enabled the average skilled person to provide DNA molecules with a deletion, substitution or insertion mutation as specified in claim 11. Moreover, while claim 11 required homologous recombination, the application failed to describe any generally applicable method of homologous recombination in higher plants, let alone specific methods to individual groups of plants at lower taxonomic levels. As indicated in documents (11), (12) and (13), at the filing date of the priority application as well as of that of the application homologous recombination was not enabled in all plants. Thus, claim 11 lacked enablement contrary to Article 83 EPC.

Article 56 EPC

The opposition division's finding of lack of inventive step with regard to the auxiliary request 3 then on file was correct and applied equally to the present requests. Document (1) was the acknowledged closest prior art document. It described two very similar, related xylosyltransferase proteins and suggested commonality via gene splicing (see passages on page 9, lines 2 and 3; page 22, line 29 to page 23, line 3; page 32, line 29 to page 33, line 5; and page 33, line 24 to page 34, line 1). On page 35, lines 19 to 26 it was suggested to prepare oligonucleotides from the peptide sequences provided therein and use them to clone the gene for the xylosyltransferase gene from a soybean library. Document (1) also referred repeatedly to the activity of carrying out a BLAST search (see page 6, lines 19 and 20; page 9, lines 3 to 5; page 23, lines 5 to 8; and page 34, lines 1 to 4).

The sole technical difference between the claims and document (1) was the provision of a nucleotide sequence that encoded an active xylosyltransferase. The objective technical problem was the provision of the clones and of the sequenced whole gene of a plant xylosyltransferase.

The opposition division had been entirely correct to decide that the average skilled person, starting with the peptide sequences of document (1), would have carried out BLAST searches, because this was the easiest and most efficient way of finding full length and/or highly related protein sequences in the public databases. Additionally, the skilled person would have been motivated to do it because it would have known about the Arabidopsis sequencing project and how it was nearing completion. The result of the obvious BLAST searching was not just finding the genomic sequence of document (2), but also identifying the sequence, in particular the coding sequence of the xylosyl transferase gene within that genomic DNA clone using tools available at the priority date. Once the gene sequence had been identified, no inventive effort or undue burden was required for expressing the gene product and testing it for xylosyltransferase activity.

Since document (1) made available a partial clone with the SEQ ID NOs: 6 and 7, it was an obvious step to use the partial sequences to screen a cDNA library of any plant, not just soybean. Routine methods would have been used. The skilled person would not be confused by the presence of "stop" codons in all three reading frames of the SEQ ID NO: 6, as it would be clear that the SEQ ID NOs: 1 to 5 obtained from sequencing the peptides represented the correct amino acid sequence of the xylosyltransferase.

As an alternative approach, the skilled person would have been able to repeat the purification procedure of document (1) and generate sufficient full length protein to sequence it and carry out a BLAST search. Another option had been to generate antibodies to the purified soybean xylosyltransferase and use them to screen a cDNA library of Arabidopsis.

Whichever of the routine approaches the skilled person might have selected, there would always have been a reasonable expectation of success in being able to isolate and clone a full length cDNA from a library. There was no evidence to prove the alleged technical difficulties when trying to obtain a full length cDNA clone from soybean. Both the patent and document (16) published by the inventors were silent on any technical difficulties, and described cloning of the Arabidopsis xylosyltransferase applying only routine genomic analysis and ordinary methods of cloning and expression.

XV. The appellant (patent proprietor) requested that the decision under appeal be set aside and that the patent be maintained on the basis of claims 1 to 17 of the new main request filed during oral proceedings and an amended description adapted thereto.

XVI. The respondent (opponent) requested in writing that the appeal be dismissed.