T 2160/18 (Beta-glucosidase/ROAL OY) 20-10-2021

Admittance of the main request into the proceedings

1. In the decision under appeal, the auxiliary request then on file was considered to fulfil the requirements of the EPC. The set of claims of the present main request, which was filed together with the respondent's reply to the statement of grounds of appeal, differs from the auxiliary request underlying the decision under appeal in that claim 2 has been deleted, and claim 10 (re-numbered as claim 9) has been amended to (i) omit from the enzyme preparation the endoglucanase defined by reference to SEQ ID NOs:10, 12, 14 and 16, and an enzymatically active fragment thereof; and (ii) require the presence of a previously optional xylanase.

2. The appellant did not oppose the admittance of the amended claims into the proceedings. As the amendments introduced into the claims were made in response to specific objections under Article 123(2) EPC raised in the statement of grounds of appeal, the board decided to admit and consider the present main request.

Rule 80 and Articles 123(2)(3), 76(1) and 84 EPC

3. The amendments introduced into the claims are occasioned by the ground for opposition of Article 100(c) EPC. Hence, the requirement of Rule 80 EPC is met.

4. In the decision under appeal, the opposition division found that the subject-matter of the claims according to the auxiliary request then on file did not extend beyond the content of either the parent application or the application as filed (see points 3.c) and d) on page 4 of the decision). The appellant contested this finding only with regard to claims 2 and 10.

5. In the present main request, claim 2 has been deleted, and claim 10 amended and re-numbered as claim 9. The appellant did not dispute that the subject-matter of amended claim 9 is disclosed in the parent application and the application as filed. As the board has no doubt that the claimed subject-matter is directly and unambiguously derivable from claims 18, 26 and 28 of the parent application; and page 6, lines 14 to 17; page 18, lines 33 to 36; and page 16, lines 3 to 5 of the application as filed, the amendments introduced into the claim are considered to conform both Article 123(2) and Article 76(1) EPC.

6. No objections were raised by the appellant with regard to Article 123(3) EPC or Article 84 EPC. The board sees no reason to raise any of its own motion.

Article 83 EPC - sufficiency of disclosure

7. In the decision under appeal, the opposition division found that the objection of lack of sufficient disclosure had not been substantiated by verifiable facts, and considered the invention as defined in claim 1 of the auxiliary request to be sufficiently disclosed in the application as filed.

8. In its statement of grounds of appeal, the appellant disagreed with the opposition division's legal reasoning and contested the findings on Article 83 EPC arguing - for the first time - that there was no evidence that "... the (incorrectly deduced) polypeptide sequence of SEQ ID NO:22 has cellulolytic activity, as the claims required". In appellant's view, the respondent "... bears the legal burden of demonstrating that the claimed polypeptide has the claimed function" (see sections 10.3 and 10.8 of the statement of grounds of appeal).

9. Annexes IA to IC, IIA and IIB were submitted by the respondent together with its reply to the statement of grounds of appeal in order to address appellant's argument. The board is satisfied that there had been no reason for the respondent to present this evidence in opposition proceedings. This has not been disputed by the appellant. Hence, having been presented in due time, Annexes IA to IC, IIA and IIB are taken into account by the board for its decision.

10. It is undisputed that the polypeptide sequence of SEQ ID NO:22 of the application as filed contains errors. Annex IA shows the nucleotide sequence and the polypeptide sequence disclosed in the application as filed as, respectively, SEQ ID NO:21 and SEQ ID NO:22; introns and CDSs are indicated. It also shows the errors in these sequences arising from an erroneous intron annotation (see page 5) and three additional nucleotides that in fact do not exist (see nucleotides C3264, T3291 and A3297 on page 6). The corrected sequence is provided for comparison. In Annex IB, the polypeptide sequence of SEQ ID NO:22 is compared to the sequence encoded by SEQ ID NO:21 disclosed in the application as filed and to the correct polypeptide sequence. Annex IC shows the comparison between the polypeptide sequence of SEQ ID NO:22 and the correct polypeptide sequence.

11. The experimental evidence in Annexes IIA and IIB shows that polypeptides produced by expressing either (i) a synthetic gene encoding the polypeptide of SEQ ID NO:22 (Annex IIA) or (ii) the nucleotide sequence of SEQ ID NO:21 (Annex IIB) inserted into an expression cassette for T. reesei, have in fact beta-glucosidase activity. As apparent from Figure 2 of each Annex IIA and IIB, the pH optimum of both beta-glucosidase enzymes is about pH 4.5.

12. This experimental evidence was not questioned by the appellant, and the board is satisfied that the burden of proving that a polypeptide having the sequence of SEQ ID NO:22 has cellulolytic activity, has been discharged.

13. As regards appellant's argument concerning the beta-glucosidase activity of variants of the polypeptide encoded by SEQ ID NO:22, the experimental results reported in Annex IIB show that the polypeptide encoded by SEQ ID NO:21, which differs from the polypeptide of SEQ ID NO:22 by 20 amino acids, i.e. is 97% identical (see Annex IB), has cellulolytic activity. The board has no doubts that a person skilled in the art at the relevant date was able to find further polypeptides having cellulolytic activity and at least 80% identity to SEQ ID NO:22, without undue burden or inventive skills.

14. Hence, having considered the arguments and evidence put forward by the parties in appeal proceedings, the board concludes that the patent application discloses the claimed invention in a manner sufficiently clear and complete for it to be carried out by the person skilled in the art. Thus, the requirements of Article 83 EPC are fulfilled.

Admittance of document (15)

15. Document (15) was filed by the present appellant three weeks before the date of the oral proceedings before the opposition division. The document purportedly confirms by way of DNA sequencing that the beta-glucosidase from T. aurantiacus described in document (4) falls within the scope of claims 1 and 2 of the patent as granted and, consequently, deprives the subject-matter of these claims of novelty (see submission of the present appellant - then opponent - dated 25 April 2018).

16. In the decision under appeal, the opposition division decided not to admit document (15) into the proceedings, on the grounds that the document had been filed late and not sent to the other party until an even later date, and that, prima facie, the experimental evidence therein did not appear to be relevant (see first full paragraph on page 5 of the decision under appeal). The appellant has contested these findings.

17. According to established case law of the Boards of Appeal, evidence first submitted by an opponent after expiry of the nine-month period under Article 99(1) EPC is generally to be regarded as not filed in due time for the purpose of Article 114(2) EPC and the opposition division has in principle discretion not to admit it. In the present case, the objection of lack of novelty in view of document (4) had been raised already in the notice of opposition. Hence, the evidence in document (15) could - and should - have been submitted within the time limit for filing an opposition pursuant to Article 99(1) EPC.

18. Even if the board were to accept appellant's argument that document (15) had been submitted in response to an observation made by the opposition division in the communication attached to the summons to oral proceedings, the document should nevertheless have been submitted, at the latest, at the date fixed by the opposition division for making written submissions in preparation for the oral proceedings under Rule 116(1) EPC, i.e. two months before the date of the oral proceedings (see last sentence on page 8 of the opposition division's communication dated 17 November 2017). Since the document was submitted only three weeks before the date of the oral proceedings, there is no doubt that document (15) was not filed in due time, and that its admission into the opposition proceedings was at the discretion of the opposition division (see Article 114(2) EPC).

19. The decision of the opposition division to disregard the late-filed document (15) could be overruled only if the board were to conclude that the opposition division exercised its discretion according to wrong principles, or without taking into account the right principles, or in an unreasonable way (see decision G 7/93, OJ EPO 1994, 775, point 2.6 of the Reasons). This is however not the case.

20. According to established jurisprudence of the Boards of Appeal, a decisive criterion to be taken into account by the opposition division when deciding on the admissibility of late-filed documents, is their prima facie relevance (see, e.g., decision T 1002/92, OJ EPO 1995, 605). As apparent from the decision under appeal, the opposition division took into account this issue and concluded that document (15) was prima facie not sufficiently relevant to change the outcome of the opposition proceedings (see section 5.c on page 5 of the decision under appeal).

21. The opposition division considered also the question whether the patent proprietor had been in a position to adequately react to the submission of document (15). In this context, the opposition division stated in its decision that document (15) had not been forwarded to the patent proprietor "until an even later date", i.e. even less than three weeks before the oral proceedings. The appellant contested this finding and submitted document (16) as evidence that document (15) had been sent via email to the other party on the same date as to the opposition division, i.e. three weeks before the oral proceedings.

22. However, document (16) filed in appeal proceedings does not call into question the exercise of discretion by the opposition division which was based on the evidence then on file. As apparent from the minutes of the oral proceedings before the opposition division, dated 27 June 2018 (see last paragraph on page 1), the patent proprietor declared that no email from the opponent had been received. In the absence of evidence on file that an email including document (15) had been sent to and received by the patent proprietor, the opposition division correctly found that document (15) became available to the patent proprietor only at a later date, i.e. when it was forwarded by the division few days before the oral proceedings.

23. In view of the above, the board is satisfied that the opposition division exercised its discretion correctly and in a reasonable way, and sees no reason to overturn the opposition division's discretionary decision not to admit document (15) into the opposition proceedings in accordance with Article 114(2) EPC.

24. Nor does the board see any reason to exercise its own discretion under Article 12(4) RPBA 2007 to admit into the appeal proceedings either document (15) or appellant's submissions relying on this document, even giving due consideration to the evidence provided in document (16) (see decisions T 971/11 of 4 March 2016, point 1 of the Reasons; and T 942/12 of 17 November 2015, point 7 of the Reasons).

25. Like the opposition division, the board holds the view that document (15) is prima facie not sufficiently relevant to change the outcome of the proceedings. The experimental evidence in document (15) might show that a nucleotide sequence encoding a polypeptide having an amino acid sequence which is at least 80% identical to SEQ ID NO:22 is present in the genome of T. aurantiacus IMI 216529. However, contrary to appellant's view document (15) does not serve to prove beyond doubt that the method described in document (4) inevitably leads to such a polypeptide.

26. Hence, document (15) was not admitted into the appeal proceedings.

Admittance of document (17)

27. Document (17), which was filed together with the statement of grounds of appeal, is a declaration of Dr Mark Wogulis, an employee of the appellant. In sections 11 to 14 of this document, Dr Wogulis makes some statements on the question whether or not it is generally thought that significant variability in the amino acid sequence of a given protein exists among different strains of a fungal species. Since this issue was brought forward by the examining division in its communication in preparation for the oral proceedings (see second and third sentence in section 3.c on page 4), the board fails to see any reason why this evidence could not have been submitted in opposition proceedings.

28. It is not clear which objection (lack of novelty or lack of inventive step) Dr Wogulis' statements in sections 5 to 10 of his declaration are intended to support. In any case, both objections were raised in the notice of opposition, and in the opposition division's communication in preparation for the oral proceedings, which was issued six months in advance of the oral proceedings, a provisional view adverse to the present appellant was expressed. Hence, the declaration of Dr Wogulis could and should have been submitted already in opposition proceedings.

29. For these reasons, the board holds the evidence in document (17) not to be inadmissible.

Article 54 EPC - novelty

30. Claim 1 of the present main request is identical to the corresponding claim of the auxiliary request underlying the decision under appeal. The opposition division regarded the subject-matter of claim 1 of the auxiliary request then on file as novel in the light of the content of documents (4) and (11). This applied also to the remaining claims which referred to claim 1 (see section 5c bridging pages 7 and 8 of the decision).

Document (4)

31. It is established jurisprudence of the Boards of Appeal that, for concluding lack of novelty, the claimed subject-matter must be directly and unambiguously derivable from the prior art. For ascertaining the disclosure of a document forming part of the state of the art within the meaning of Article 54(2) EPC, the relevant date is the date of its publication (see T 205/91 of 16 June 1992, T 737/00 of 21 May 2003, and T 1162/07 of 6 October 2010). It has to be beyond doubt - not merely probable - that the disclosure in the state of the art would inevitably lead to subject-matter falling within the scope of the claim.

32. Document (4) describes the purification and biochemical characterization of an extracellular thermostable beta-glucosidase from Thermoascus aurantiacus IMI 216529. The beta-glucosidase was purified to homogeneity by DEAE-Sepharose, Ultrogel AcA 44 and mono-P column chromatography (see Abstract and paragraph bridging pages 119 and 120). The enzyme is said to be a homotrimer, with a monomer molecular mass of 120 kDa, the trimer being optimally active at 80°C and at pH 4.5 (see Abstract and page 120, left-hand column). In Figure 8, an N-terminal sequence of 20 amino acid residues of the beta-glucosidase is described. Based on the high degree of N-terminal sequence identity with other beta-glucosidases, the authors of document (4) suggest that the enzyme could be a member of glycoside hydrolase family 3 (see Abstract and page 126, right-hand column, second sentence of the last paragraph).

33. It is undisputed that document (4) does not explicitly report the complete sequence of the isolated beta-glucosidase, and that only 11 amino acid residues out of the N-terminal sequence of 20 amino acid residues described in document (4) are identical to a sequence in SEQ ID NO:22 of the present patent, whereas the amino acids at positions 1 and 13 to 20 differ between the two sequences. Hence, like the opposition division, the board holds that the sequence data provided in document (4) do not allow to establish without doubt the identity between the beta-glucosidase described therein and that defined in claim 1.

34. Relying on document (7), the appellant argued that the differences between the sequence provided in document (4) and that of SEQ ID NO:22 were clearly due to inaccuracies in the sequencing technique used in document (4). However, for the purpose of examining novelty, document (4) is to be assessed from the perspective of a person skilled in the art at the publication date. The skilled person does not find in document (4) any indication whatsoever of possible errors in the amino acid sequence provided therein, let alone which partial sequence might be erroneous. Thus, there was no reason for the skilled person at the publication date of document (4) to suspect that the amino acid sequence provided therein contained any errors.

35. For its finding on novelty, the opposition division took into account also differences between the beta-glucosidase polypeptide described in document (4) and that of the invention as regards the molecular weight (120 kDa vs. 81 kD) and the optimal temperature (80°C vs. 75°C). The appellant tried to explain the striking difference in molecular weight on the basis of simple error and/or different levels of glycosylation. However, a person skilled in the art cannot derive from document (4) any indication for a potential error when determining the molecular weight of the beta-glucosidase polypeptide described therein. Nor is there any mention in document (4) of a possible glycosylation of the polypeptide.

36. Further, the appellant relied on post-published documents (2) and (3) to support its contention that T. aurantiacus produces only two beta-glucosidases, of which only one is thermostable. In appellant's view, the thermostable beta-glucosidase polypeptides described in documents (4) and (2) must be the same as the beta-glucosidase polypeptide of the invention.

37. This argument is not persuasive. Document (12), on which the appellant relied for inventive step, describes three beta-glucosidases in T. aurantiacus (see Figure 1), and characterises two of them (Gl-2 and Gl-3) as being thermostable and having different pH and temperature optima. Moreover, it is apparent from document (8) that, based on the post-published sequence of the genome of T. aurantiacus, up to eight putative beta-glucosidases may be produced in this organism.

38. In the board's view, document (2) - and document (8) - may show that a nucleotide sequence encoding a polypeptide having an amino acid sequence which is at least 80% identical to SEQ ID NO:22 is present in the genome of T. aurantiacus. However, these documents do not prove beyond doubt that carrying out the method described in document (4) inevitably leads to a polypeptide with beta-glucosidase activity and having an amino acid sequence at least 80% identical to SEQ ID NO:22.

39. Similarly, the experimental evidence in documents (13) and (14) may show that a polypeptide having beta-glucosidase activity and sharing several partial amino acid sequences with SEQ ID NO:22 of the patent is present in T. aurantiacus IMI 216529, which is the same strain used in document (4). However, in view of the fact that T. aurantiacus appears to produce several beta-glucosidases (see document (12)), and that the method used in document (13) for isolating the beta-glucosidase polypeptide from which the partial amino acid sequences are obtained, differs substantially from the method used in document (4), documents (13) and (14) cannot be considered to prove beyond doubt that carrying out the method described in document (4) inevitably leads to a polypeptide having beta-glucosidase activity and an amino acid sequence which is at least 80% identical to SEQ ID NO:22.

40. For these reasons, novelty over document (4) is acknowledged.

Document (11)

41. Document (11) describes a thermostable beta-glucosidase with a molecular weight of 87 kDa which is optimally active at pH 4.5-5.0. However, document (11) does not provide any amino acid sequence and there is no proof that carrying out the method described in this document inevitably leads to a beta-glucosidase falling within the scope of claim 1. As stated above, it is apparent from document (12) that T. aurantiacus produces at least two thermostable beta-glucosidases. It is stated in this document that the method described in document (11) for the purification of the thermostable beta-glucosidase "... was not efficient in separating the [two] enzymes", and that ion-exchange chromatography was crucial (see document (12), page 688, lines 1 to 5, and the reference to Tong et al. (1980) which is document (11) in the present proceedings). Since the method described in document (11) does not involve ion-exchange chromatography for the purification of the beta-glucosidase, it is uncertain which enzyme(s) result(s) from carrying out the described method. Thus, a polypeptide as defined in claim 1 cannot be considered to be directly and unambiguously derivable from document (11).

42. Consequently, also novelty over document (11) is acknowledged.

Article 56 EPC - inventive step

Document (4) as the closest state of the art

43. It is common ground that, starting from document (4) as the closest state of the art, the technical problem to be solved is the provision of an alternative thermostable beta-glucosidase from T. aurantiacus. Hence, for assessing inventive step the question whether or not the claimed polypeptide shows any advantageous properties compared to the polypeptide described in document (4) does not need to be considered, contrary to appellant's view.

44. In view of the experimental evidence in the examples of the patent and Annexes IIA and IIB, there is no doubt that the problem is solved by a polypeptide as defined in claim 1.

45. Having considered the arguments put forward by the appellant, the board is not persuaded that a person skilled in the art relying on the information given in document (4) would have arrived at a polypeptide as claimed in an obvious manner.

46. The appellant argued that providing the same beta-glucosidase already isolated and characterized in document (4) was obvious. However, as discussed in the context of novelty above, the appellant failed to provide convincing evidence that the polypeptide isolated in document (4) was in fact the same as the polypeptide of SEQ ID NO:22, or that a person skilled in the art applying the method described in document (4) would have isolated a polypeptide as defined in claim 1. As document (4) teaches a beta-glucosidase polypeptide with a molecular weight of 120 kD, it was in fact obvious to the skilled person to try to isolate such a polypeptide. However, document (4) does not teach or suggest that T. aurantiacus may produce other beta-glucosidases, and without knowledge of the present invention, the skilled person would not have expected to isolate a further beta-glucosidase polypeptide with a substantially lower molecular weight, let alone the specific polypeptide defined in claim 1. The appellant failed to substantiate convincingly its allegation that the skilled person would not place particular significance on the molecular weight reported in document (4).

47. Also appellant's argument that the skilled person could have used the sequence information provided in document (4) to clone a nucleic acid encoding the described polypeptide, is unconvincing. The board shares the respondent's view that the amino acid sequence described in document (4) would not be sufficient to allow the skilled person to design PCR primers. As regards hybridization with a degenerated probe designed on the basis of the amino acid sequence described in document (4), in view of the substantial differences between that sequence and the sequence of SEQ ID NO:22 (see paragraph 33 above) it is highly doubtful whether the skilled person would be able to isolate, without undue burden, a nucleotide sequence encoding the claimed polypeptide.

48. For these reasons, the subject-matter of claim 1 cannot be regarded as obvious in view of the teachings of document (4).

Document (12) as the closest state of the art

49. Document (12) describes the partial purification and characterization of two thermostable beta-glucosidases (GI-2 and GI-3) from T. aurantiacus having a molecular weight of 175 kD and 157 kD, respectively (see Abstract). There is no evidence on file that the thermostable GI-2 and GI-3 beta-glucosidase polypeptides characterized in document (12) may have any similarity to the polypeptides of the invention. The fact that their molecular weight differs substantially from the molecular weight of the polypeptide isolated by the present inventors appears to indicate that they are in fact different polypeptides. Document (12) does not provide any sequence information for the characterized beta-glucosidases.

50. Starting from document (12), the technical problem to be solved is the provision of an alternative thermostable beta-glucosidase from T. aurantiacus. The solution is a polypeptide as defined in claim 1.

51. Since document (12) described at least two beta-glucosidase polypeptides in T. aurantiacus, the skilled person could have attempted to isolate a further polypeptide applying the purification method described in document (12), as it is apparent from Figure 1 of this document that a third fraction (GI-1) having beta-glucosidase activity was eluted from the anion-exchanger column. There is however no evidence on file showing that the third fraction described in document (12) contained a polypeptide as defined in claim 1, and the appellant did not argue to this effect.

52. The appellant did not put forward any arguments as to which obvious course of action would have been taken by the skilled person, starting from document (12), to arrive at the claimed beta-glucosidase polypeptides in an straightforward manner. Rather, the appellant substantiated its objection of lack of inventive step basically by referring to decision T 823/12 of 23 August 2016 and decision T 386/94 of 11 January 1996. The facts underlying the cited decisions differ however from the facts in the present case.

53. In decision T 823/12 (supra), which relates to polypeptides having cellulolytic enhancing activity produced by the filamentous fungus Thielavia terrestris, the document considered to be the closest state of the art ("D1") described the identification and cloning of five genes encoding such polypeptides, by applying an experimental procedure which involved the use of EST sequences to identify sequences encoding the desired polypeptides. In the application then at issue, the same experimental procedure was applied for identifying and cloning a further gene coding for a polypeptide having cellulolytic enhancing activity from the same fungus. The board found that the fact that the closest state of the art "... had already disclosed that 13 genes from the assembled EST sequences had hits against known glycosyl hydrolase genes [...] justified the reasonable expectation that there were more glycosyl hydrolase genes in Thielavia terrestris than the five which were cloned in D1" (see point 2.5 of the Reasons). Thus, the board concluded that the claimed polypeptides did not involve an inventive step.

54. In the present case, document (12) describes the isolation and characterization of two beta-glucosidase polypeptides from T. aurantiacus, but does not suggest, let alone expressly indicates that T. aurantiacus may produce further thermostable beta-glucosidases. Nor does document (12) provide any sequence data on the basis of which the skilled person could have identified genes encoding further beta-glucosidase polypeptides. Instead of the purification method described in document (12), the present invention uses a different approach to isolate the beta-glucosidase polypeptide with the degree of purity required for peptide sequencing. While this may appear trivial, given the large amount of different polypeptides secreted by cellulolytic fungi it is not. In view of these factual differences, the board does not deem the conclusion of lack of inventive step in decision T 823/12 (supra) applicable to the present case.

55. To support its allegation that the cloning and expression of the claimed beta-glucosidase using standard methods could not be inventive, the appellant cited the Headnote of decision T 386/94 (supra). However, the factual situation underlying the cited decision cannot be compared to that in the present case. Decision T 386/94 (supra) relates to a process for producing chymosin polypeptide or its precursors which involves the cloning and expression of a DNA sequence encoding the polypeptides. The document representing the closest state of the art described the chymosin polypeptide and its precursor prochymosin, as well as the isolation of a recombinant clone containing sufficient cDNA to code for 80% of the prochymosin polypeptide (se point 25 of the Reasons). The competent board found that a person skilled in the art would have perceived the cloning and expression of the chymosin DNA "... as an endeavour likely to succeed and that achieving this cloning did not pose such problems as to prove that this assumption was wrong". Consequently, the board concluded that the claimed process did not involve an inventive step (see point 42 of the Reasons).

56. In decision T 386/94 (supra), chymosin and its precursors were well-characterised polypeptides, their amino acid sequence was known and a DNA molecule encoding 80% of the precursor prochymosin had been isolated, the actual achievement of the claimed invention being the cloning and expression of the complete DNA sequence. In contrast, in the present case it was uncertain at the relevant date whether T. aurantiacus produced further beta-glucosidase polypeptides, further polypeptides had not been characterized, their amino acid sequence was unknown and a DNA sequence encoding them had not been identified. As these facts differ substantially from those in decision T 386/94 (supra), the board's conclusion in that decision cannot apply to the present case.

57. Summarising the above: the arguments put forward by the opponent to substantiate its objection of lack of inventive step over document (12) fail to persuade the board.

Adaptation of the description

58. At the oral proceedings before the board, the respondent submitted amended pages 10 and 11 of the patent to adapt the description to the amended claim 9.