T 1644/08 (Endoglucanases/NOVOZYMES) 15-02-2011

Summary of Facts and Submissions

I. An appeal was lodged by the opponent (appellant) against the decision of the opposition division, whereby the opposition against the European patent No. 0 815 209 was rejected. The opposition division considered that none of the grounds of opposition under Articles 100(a) and 100(c) EPC prejudiced the maintenance of the patent as granted.

II. The opposed patent was based on the European patent application No. 96 905 762.9 which was published as International patent application WO 96/29397 (hereinafter "the application as filed"). The patent application contained 104 claims, wherein claims 72 and 89 read as follows:

"72. A DNA construct comprising a DNA sequence encoding an enzyme exhibiting endoglucanase activity, which DNA sequence comprises

a) the DNA sequence shown in SEQ ID No. 8, or the DNA sequence obtainable from the plasmid in Saccharomyces cerevisiae DSM 10081, or

b) an analogue of the DNA sequence shown in SEQ ID No. 8 or the DNA sequence obtainable from the plasmid in Saccharomyces cerevisiae DSM 10081, which

i) is homologous, preferably at least 75% homologous, with the DNA sequence shown in SEQ ID No. 8 or the DNA sequence obtainable from the plasmid in Saccharomyces cerevisiae DSM 10081,

ii) hybridizes under the conditions described herein with the same nucleotide probe as the DNA sequence shown in SEQ ID No. 8 or the DNA sequence obtainable from the plasmid in Saccharomyces cerevisiae DSM 10081,

iii) encodes a polypeptide which is homologous, preferably at least 70% homologous, with the polypeptide encoded by a DNA sequence comprising the DNA sequence shown in SEQ ID No. 8 or the DNA sequence obtainable from the plasmid in Saccharomyces cerevisiae DSM 10081,

iv) encodes a polypeptide which is immunologically reactive with an antibody raised against the purified endoglucanase encoded by the DNA sequence shown in SEQ ID No. 8 or obtainable from the plasmid in Saccharomyces cerevisiae, DSM 10081."

"89. An enzyme exhibiting endoglucanase activity, which enzyme

a) is encoded by a DNA construct according to any of claims 66-83,

b) produced by the method according to claim 88, or

c) is immunologically reactive with an antibody raised against a purified endoglucanase encoded by the DNA sequence shown in any of the sequence listings SEQ ID No 1, 4, 6, 8, 10, 12, 16, 19."

III. With its statement of grounds of appeal, the appellant filed two experimental reports.

IV. The patentee (respondent) replied to the appellant's grounds of appeal and filed six auxiliary requests, further documents and experimental evidence.

V. Further submissions were also filed by the appellant commenting on the respondent's new claim requests.

VI. The board issued a summons to oral proceedings to which a communication was attached. In that communication the parties were informed of the board's preliminary, non-binding views on the issues to be discussed at the upcoming oral proceedings.

VII. Both the appellant and the respondent replied to the communication of the board and filed further documents and experimental evidence. While the respondent filed a new main request and six new auxiliary requests, the appellant commented on these new claim requests.

VIII. In reply to the appellant's comments, the respondent submitted further observations and documents.

IX. Oral proceedings took place on 15 February 2011. At these proceedings, the respondent withdrew all its previous claim requests and filed a new main request mainly based on the previous auxiliary request 4.

X. The respondent's main request consisted of 21 claims. Claim 1 read as claim 72 of the application as filed (supra) with part (b) contemplating only two alternatives i) and ii):

"1. ...

i) has at least 90% identity with the coding region of the DNA sequence shown in SEQ ID No. 8 or the DNA sequence obtainable from the plasmid in Saccharomyces cerevisiae DSM 10081, or

ii) encodes a polypeptide which has at least 90% identity with the polypeptide encoded by a DNA sequence comprising the DNA sequence shown in SEQ ID No. 8 or the DNA sequence obtainable from the plasmid in Saccharomyces cerevisiae DSM 10081."

Claim 10, which corresponded to claim 89 of the application as filed (supra) but contemplated only two alternatives a) and b), read as follows:

"10. An enzyme exhibiting endoglucanase activity, which enzyme is

a) encoded by a DNA construct according to any of claims 1-4, or

b) at least 90% identical to the amino acid sequence shown in SEQ ID No. 9."

Claims 2 to 4 related to particular embodiments of claim 1. Claim 5 concerned a recombinant expression vector comprising a DNA construct according to any of claims 1 to 4. Claims 6 to 8 were directed to a cell comprising a DNA construct of any of claims 1 to 4 or a vector according to claim 5. Claim 9 related to a method of producing an enzyme exhibiting endoglucanase activity comprising culturing a cell of any of claims 6 to 8. Claims 11 and 17 concerned a method of providing colour clarification of laundry and a laundry composition, respectively, wherein both claims referred to an enzyme according to claim 10. Claims 12 to 16 and claims 18 to 20 were particular embodiments of claims 11 and 17, respectively. Claim 21 was directed to the use of the enzyme according to claim 10 for treatment of fabric or textile, preferably for preventing backstaining, for bio-polishing or for "stone-washing" cellulosic fabric.

XI. The following documents are cited in the present decision:

D1: WO 91/17243 (publication date: 14 November 1991);

D6: WO 94/07998 (publication date: 14 April 1994);

D7: P.O. Sheppard et al., Gene, 1994, Vol. 150, pages 163 to 167;

D8: C. Breuil et al., Biotechnol. Letters, 1986, Vol. 8, No. 9, pages 673 to 676.

XII. The arguments of the appellant, insofar as they are relevant to the present decision, may be summarised as follows:

Admissibility of the main request

The main request was based on an auxiliary request that was filed shortly in advance of the oral proceedings and, thus, was late filed. Moreover, the main request could have been filed at a much earlier stage of the proceedings since it intended to overcome an objection for lack of novelty that was on file from the beginning of the opposition proceedings. According to the established case law, the patentee's right to file amendments is not unlimited (cf. T 1898/07 of 17 June 2010, point 2 of the Reasons and T 363/99 of 19 April 2004, point 2 of the Reasons) and good reasons have to be provided for the late filing of amendments.

Main request

Article 123(2) EPC

The application as filed referred to several degrees of identity, including 90% identity. However, they were always linked to the GAP computer program and the 'GAP creation and extension penalties' settings used for their calculation. Moreover, there was no specific sequence singled out among all the sequences, (SEQ ID NO), disclosed. Although claim 1(b) i) and ii) referred to a 90% identity, the computer program and settings were not specified. There was no basis in the application as filed for singling out a specific SEQ ID NO and a degree of identity, let alone for combining them.

Nor was a basis in the application as filed for feature a) of claim 10 in isolation. Original claim 89 required the endoglucanase to be encoded by a DNA construct but, in line with the disclosure found in the description of the application as filed, such as on page 32, lines 5 to 15, it also required the enzyme to be produced by a particular method and/or to have particular immunological properties. Claim 10 b) had no basis in the application as filed since its wording was different from that found in the description of the application as filed, such as on pages 30 and 31.

Article 84 EPC

The analogues of SEQ ID NO:8 were defined in the application as filed as having the characteristics cited in original claim 72(b) i) to iv) and being at least 75% homologous with SEQ ID NO:8. Claims 1 and 10 of the main request did not contemplate these characteristics and required the analogues to have at least 90% identity. Thus, the products of claims 1 and 10 were not fully characterized and essential features were missing from these claims. Moreover, there was no indication as how the degree of identity was calculated or whether the degree was over the full length of the coding region or over only parts thereof.

Article 54 EPC

The endoglucanase of claim 10 was at least 90% identical to SEQ ID NO:9 which itself had a high degree of identity to the endoglucanases from Humicola insolens DSM 1800 and from Fusarium oxysporum DSM 2672 of document D1. Sequence alignments filed with the notice of opposition showed long stretches of identity among these sequences. The teachings of document D1 were not limited to these sequences but contemplated homologues exhibiting endoglucanase activity and being encoded by DNA which hybridized to the same probe as the DNA coding for these specific endoglucanase enzymes, such as stated on page 4, lines 24 to 32 of document D1. Probes could be based, for instance, on the oligonucleotides listed in Table 1 of document D1 (cf. pages 34 to 35) and on regions having identity stretches such as those shown in the sequence alignments filed with the grounds of opposition. Probes hybridizing to a DNA encoding the endoglucanase from Thielavia terrestris would certainly have hybridized with DNA sequences encoding homologues of the endoglucanases shown in document D1. Thus, these homologues fell within the scope of claims 1 and 10 of the main request. According to decision T 1120/00 of 22 October 2004, if a prior patent application disclosed not only a specific DNA sequence but also homologues thereof, claims in a latter patent application were novel over such a disclosure only if they excluded all these DNA sequences in their entirety. If there was an area of overlap between this prior art and the claimed subject-matter, novelty was not acknowledged.

Article 56 EPC

Document D6, the closest prior art, related to variants of known cellulases with improved properties when used in detergent compositions. Several cellulases were described as suitable parent cellulases, including the endoglucanase from Humicola insolens DSM 1800. Starting from this prior art, the technical problem to be solved was the provision of further endoglucanases for use in detergent compositions. The invention as claimed in the main request provided a solution to this technical problem.

However, this solution was obvious. Document D6 identified the endoglucanase from Humicola insolens DSM 1800 as a cellulase of the family 45 (cf. page 9, lines 26 to 30). Members of that family were known to share regions of highly conserved amino acids - as shown in Figure 1 of document D6 - and, based on these regions, probes could be designed and used to isolate new family members. Indeed, suitable probes for members of the cellulase family 45 - or the K-family - were shown in Figure 1 of document D7, a document which was part of the common general knowledge. In line with decision T 875/02 of 7 December 2004, once a perfect probe was available to the skilled person, cloning of the full-length gene was obvious. The quality of the probe shown in Figure 1 of document D7 and its suitability for cloning a DNA sequence encoding the endoglucanase from Thielavia terrestris had never been challenged.

Several Thielavia terrestris strains were known to be among the most cellulolytic strains from various culture collections of thermophilic fungi and Thielavia terrestris strain NRRL 8126 was known to have a high cellulase activity. Document D8 reported the presence in this latter strain of a high amount of thermostable endoglucanase activity with a good half-life at 60ºC, a temperature known to be normally used in washing operations. This temperature was thus a clear pointer for the skilled person who would immediately have considered the endoglucanase from Thielavia terrestris NRRL 8126 of document D8 to be suitable for detergent compositions as those described in document D6. Knowing these advantageous properties of the endoglucanase from Thielavia terrestris NRRL 8126, it was obvious to use the tools available from document D6 (or the probe from document D7) in that strain and obtain thereby the claimed subject-matter. No technical problems would have been encountered by the skilled person as shown in the patent-in-suit. The alleged presence of several endoglucanases in Thielavia terrestris NRRL 8126 was shown in post-published documents. These documents would not have prevented the skilled person from using the probe of document D7 and identifying the endoglucanase of the family 45 in that strain. Arguments relying on post-published documents were based on an ex post facto analysis and, thus, were not to be taken into account.

In view of the deficiencies of the respondent's experimental reports (inter alia, they were not performed at optimal pH conditions for each of the compared endoglucanases (6.0-10.0 for Humicola insolens and 5.0-7.0 for Thielavia terrestris), the enzyme dosage was not indicated, the substrate was inappropriate or undefined, etc.), there was no evidence on file to show the advantageous properties of the endoglucanase from Thielavia terrestris NRRL 8126 - and certainly not for all the enzymes falling within the scope of the claims. Moreover, if an advantageous property was to be acknowledged, then it was a mere bonus effect because it was inherent to that endoglucanase, which was itself obvious from the combination of documents D6 and D8 - with document D7 as common general knowledge.

XIII. The arguments of the respondent, insofar as they are relevant to the present decision, may be summarised as follows:

Admissibility of the main request

In the board's communication, the arguments for lack of novelty over document D1 were different from those raised in opposition proceedings. In order to overcome this objection, a new feature was introduced into the claim requests filed in advance of the oral proceedings. It was at the oral proceedings that this feature was discussed for the first time and reasons given to explain the problems arising from its introduction. The main request intended to overcome these problems, it was based on one of the auxiliary requests filed in advance of the oral proceedings and it was a clear limitation of the granted claims.

Main request

Article 123(2) EPC

The DNA sequence and the encoded endoglucanase from Thielavia terrestris (SEQ ID NO:8, 9) were disclosed in an individualized form in the application as filed, such as in the examples and in original claim 72. A preferred range of 90% identity was also disclosed for all the embodiments of the invention, including that of claim 72 (SEQ ID NO:8). The combination of SEQ ID NO:8 and 90% identity was thus directly derivable from the application as filed.

Several computer programs were available to the skilled person for calculating degrees of identity. The application as filed referred to the GAP program only as an example of a program but was not intended to be limited thereto. Whereas several preferred degrees of identity were indicated, 90% was the most preferred. It was also known to the skilled person that at a higher degree of identity, the particular computer program used was less relevant, since less differences were to be accommodated.

The features of claim 10 had a basis in original claims 72 and 89 a). While feature a) had a further basis in page 32, lines 5 to 15 of the application as filed, feature b) was further supported by page 31, lines 1 to 18 and page 32, lines 32 to 33, wherein the term "enzyme" was defined as including homologues that were further characterized by a preferred degree of identity of at least 90%.

Article 84 EPC

The wording of claims 1 and 10 of the main request was identical to that of the granted claims except for the degree of identity. Thus, appellant's objection for lack of clarity should not be allowed into the appeal proceedings. In any case, the analogues of original claim 72 b) were not required to have all the features i) to iv) mentioned in that claim. The description of the application as filed stated - with reference to the properties i) to iv) - that the endoglucanases had "any or all" of them, such as on page 26, last paragraph combined with page 23, lines 9 to 37. Thus, no features were missing from claims 1 and 10. Moreover, methods to calculate the degree of identity among different sequences were known to the skilled person. Evidence was also on file showing that, when drafting patent applications, it was normal to refer to degrees of sequence identity without indicating any computer program. The skilled person knew that, at a higher degree of identity, the particular computer program used was also less relevant.

Article 54 EPC

Document D1 disclosed the endoglucanases from Humicola insolens DSM 1800 and from Fusarium oxysporum DSM 2672. None of them fell within the scope of claims 1 and 10. Although homologues of these enzymes were defined as being encoded by DNA that hybridized to the same probe as the DNA coding for these specific endoglucanases, there was no disclosure in document D1 of a probe common to the endoglucanases of that document and to that of the patent-in-suit. In order to design such a probe, it was necessary to identify identity stretches between these sequences and, thus, hindsight knowledge of the patent-in-suit was required. Apart from the oligonucleotides shown in Table 1 of document D1, all references to probes were of a general character only. There were many other regions - on which to base the design of probes - different from those showing identity stretches in the sequence alignments filed with the grounds of opposition. Moreover, it was not certain whether the undefined area (hybridizing homologues) around the specific endoglucanases of document D1 overlapped with the subject-matter of claims 1 and 10. According to the case law, the correct standard to apply when deciding novelty was on the basis of a direct and unambiguous disclosure. The factual situation underlying the decision T 1120/00 (supra) was different from that of the present case. The claimed subject-matter was specifically defined and clearly restricted by reference to a limited degree of (90%) identity.

Article 56 EPC

Document D6, the closest prior art for the assessment of inventive step, concerned variants of known cellulases obtained by mutating the DNA sequences encoding them. Although parent cellulases derived from several organisms were cited, Thielavia or Thielavia terrestris were not mentioned. Starting from this prior art, the technical problem to be solved was the provision of endoglucanases active at a broad pH range. The endoglucanase from Thielavia terrestris was shown to have an activity above 50% at a broad (5.0 to 9.0) pH range and, thus, to solve the technical problem.

There was no reference in document D6 to the Thielavia strains from document D8, although the latter was published eight years earlier than the former. None of the prior art documents concerning detergent cellulases or endoglucanases suggested Thielavia as a possible source for these enzymes. Many organisms were known to produce cellulases in a multi-enzyme cellulase system, i.e. to express several cellulases of different types. There was a vast range of possible sources and the selection of Thielavia was not comparable to what was called a "one way-street" situation. Document D8 disclosed a complex cellulase system with several components (glucosidase, cellulases), including an endoglucanase activity. However, it was not known whether this activity was derived from a single or from several endoglucanases nor was any cellulase family identified. There was evidence on file showing the presence of several endoglucanases in Thielavia terrestris and thus, even if the teachings of documents D6 and D8 were combined, the skilled person would not have inevitably arrived at the claimed subject-matter.

Although the endoglucanase activity was shown to be thermostable in document D8, there was no information whether this activity was stable over a broad pH range. There was no reference to detergents in document D8, which was only concerned with the bioconversion of lignocellulosic residues. For the degradation of cellulose to sugar, the activity of all components of the cellulase system (glucosidases, cellobiohydrolases and endoglucanases) was required. The teachings of document D8 were thus in a different technical field than that of document D6 and the patent-in-suit. In the absence of any pointer, their combination was not obvious and required hindsight knowledge of the patent-in-suit. There was no motivation to choose the probe of document D7 for cellulases of the family 45 (K-family), select Thielavia terrestris from all other possible sources available in the art and use the probe in that strain. For assessing inventive step, it was not a question whether the skilled person could have made all these choices but whether it would have made them.

The advantageous properties of the endoglucanase from Thielavia terrestris were shown in the patent-in-suit and corroborated by experimental evidence on file. This endoglucanase was shown to have a superior activity at a broader (5.0 to 9.0) pH range and, thus, to be functional at standard (pH) conditions of known (washing) processes. For an industrial process, it was normal to assess enzymatic activities at its standard (pH) conditions and not to adapt the normal conditions of this process to the optimal (pH) conditions of the enzymes. The limitation of the claims to endoglucanases with at least 90% identity to that from Thielavia terrestris was reasonable and there was no evidence on file to show that this group of enzymes did not have the same advantages as those shown by the specific endoglucanase.

XIV. The appellant (opponent) requested that the decision under appeal be set aside and that the patent-in-suit be revoked.

XV. The respondent (patentee) requested that the decision under appeal be set aside and that the patent be maintained upon the basis of claims 1 to 21 of the main request filed during the oral proceedings on 15 February 2011.