DSM NV v Novo Nordisk A/S
[2001] APO 33
•19 July 2001
OFFICIAL NOTICE
DECISION OF A DELEGATE OF THE COMMISSIONER OF PATENTS
Application : No. 671710 in the name of DSM NV
Title: Cloning and Expression of Xylanase B
Action: Opposition under section 59 by Novo Nordisk A/S
Decision: Issued .
Abstract
The opponent succeeds in its opposition to the patent application.
None of the claims are found to be inventive in the light of EP 463706. While the design of the probe may have been difficult and risky, it is considered that this was achieved by no more than routine experimentation.
Claim 1, in so far as it does not define that the enzyme must have the "specific activity" of the Aspergillus tubigensis XYL B enzyme and that the hybridisation is done under stringent conditions, is not novel in the light of the documents Törrönen and Shareck.
Claims 10-14 and 16-17 are considered not fairly based on the matter disclosed in the specification.
The application is refused. Costs are awarded against the applicant.
PATENTS ACT 1990
DECISION OF A DELEGATE OF THE COMMISSIONER OF PATENTS
Re:Patent Application No. 671710 by DSM NV and opposition under section 59 by Novo Nordisk A/S
BACKGROUND
Gist-Brocades NV filed Australian application 671710 under the provisions of the PCT on 24 December 1993. The application claimed priority from EP basic application 92204092 filed on 24 December 1992. The application was subsequently assigned under s113 to DSM NV. The transfer of interest was filed on 2 December 1998.
The Australian application was advertised accepted on 5 September 1996 and on 5 December 1996, Novo Nordisk A/S filed a notice of opposition. Evidence was completed on 6 December 1999 and the matter heard on 7 and 8 September 2000 in Canberra.
The applicants were represented by Dr Debra Yin Foo, assisted by Mr Chris Schlicht of Phillips Ormonde and Fitzpatrick, patent attorneys, Melbourne. The opponents were represented by Ms Katrina Howard of counsel assisted by Mr John McCann and Mr David Myers of Spruson and Ferguson, patent attorneys, Sydney.
THE SPECIFICATION
The invention is described as the cloning and overexpression of a DNA sequence encoding a protein having the activity of the Aspergillus tubigensis xylanase B (XYL B) protein.
The specification discloses that multiple xylanases of various molecular weights are known to be produced from a range of microorganisms including Aspergillus niger and Aspergillus tubigensis. The specification admits that it is known that microbial xylanases are always produced together with other unwanted or unneeded enzymes. It is further admitted that it is known that the cloning of the gene encoding a desired enzyme and overexpressing it in its natural host or other compatible expression host will specifically enhance the production of the enzyme of interest (page 3 line 28 - page 4 line 5).
The specification discloses that it is known to clone the A. tubigensis xylanase A (XYL A) gene and incorporates by reference the entire disclosure of EP application 91205944.5, publication number 0 463 706 A1. This document discloses the identification and partial purification of two endoxylanase enzymes, one of which is characterised as xylanase A having an apparent molecular weight of 24 kDa and an isoelectric point of lower than pH 3.5. The DNA encoding this enzyme is cloned, sequenced and expressed. The second endoxylanase (referred to as xylanase B in the current application) shows an apparent molecular weight of 22 kDa and an isoelectric point of approximately pH 4.0 (page 10, lines 30-40 of EP 463706).
The specification states that it has been found that the xylanase B enzyme has a slightly higher pH and temperature optima than xylanase A and this makes it desirable for certain applications such as the bleaching of lignocellulosic pulp where it would also be desirable to have little or no cellulase activity.
The specification states that the problems with the prior art are 1) producing xylanase B via classical fermentation and purification techniques is economically unfeasible and 2) attempts to clone the XYL B gene using heterologous hybridisation to XYL A failed (page 4 lines 24 -29).
The specification as accepted contains 17 claims, which read as follows:
1. A purified and isolated DNA sequence which encodes a polypeptide having the activity of the Aspergillus tubigensis XYL B enzyme, wherein the DNA sequence is selected from the group consisting of:
a) a DNA sequence of fungal origin as described in Figure 2;
b) genetic variants of the sequence of part a);
c) DNA sequences capable of hybridising to either one of the sequences of part a) and b), above
d) a DNA sequence which encodes a polypeptide as described in Figure 2.
e) a XYL B-encoding DNA sequence originating from Aspergillus tubigensis.
2. A DNA construct including a DNA sequence according to claim 1, operably linked to regulatory regions capable of directing the overexpression of a polypeptide having xylanase activity in a suitable expression host.
3. The DNA construct of claim 2, wherein the regulatory region includes one or more of the following characteristics: a promoter selected from the group consisting of the promoter originating from an amyloglucosidase gene and the promoter native to a xylanase gene; a secretion leader sequence selected from the group consisting of the secretion leader sequence originating from an amyloglucosidase gene and the secretion leader sequence native to a xylanase gene.
4. A transformed microbial host capable of the overexpression of a polypeptide having the activity of the Aspergillus tubigensis XYL B enzyme, wherein the microbial host contains an expression construct according to claim 2 or claim 3.
5. The transformed microbial host of claim 4, wherein the microbial host is selected from the genera consisting of Aspergillus, Kluyveromyces, Trichoderma, Saccharomyces and Bacillus.
6. A method for the overexpression of a polypeptide having xylanase activity including the steps of:
a) culturing a microbial host according to claim 4 under conditions conducive to the expression of the gene encoding the polypeptide having XYL B activity; and
b) recovering the polypeptide having XYL B activity.,
7. A polypeptide having XYL B activity wherein the polypeptide is produced by the method of claim 6.
8. Use of a polypeptide having XYL B activity according to claim 7 in the degradation of a xylan-containing substrate.
9. plM170 (CBS 629.92) as hereinbefore described.
10. Purified and isolated expression and transcription regulatory regions as found in the 5' non-coding sequence of the Aspergillus tubigensis xln B gene.
11. A Total Chlorine Free pulp bleaching sequence wherein an enzymatic step is used employing an enzyme encoded by the DNA sequence of any one of claims 1 to 3.
12. An Elementary Chlorine Free pulp bleaching sequence wherein an enzymatic step is used employing an enzyme encoded by the DNA sequence of any one of claims 1 to 3.
13. A Totally Chlorine Free (TCF) bleaching sequence represented by XWQP, representing the following steps:
enzyme incubation (X), washing (W), chelating (Q) and peroxide bleaching (P) wherein the enzyme used in step X is encoded by the DNA sequence of any one of claims 1 to 3.
14. An Elementary Chlorine Free (ECF) bleaching sequence represented by XD100ED representing enzyme incubation (X); the chlorine dioxide (D) and the alkaline extraction (E) wherein the enzyme used in step X is encoded by the DNA sequence of any one of claims 1 to 3.
15. A purified and isolated DNA sequence substantially as hereinbefore described with reference to the examples.
16. A Totally Chlorine Free (TCF) bleaching sequence substantially as hereinbefore described with reference to example 5.
17. An Elementary Chlorine Free (ECF) bleaching sequence substantially as hereinbefore described with reference to example 5.
EVIDENCE
Evidence in support consists of statutory declarations from:
John Francis McCann, Patent Attorney of Sprusons and Ferguson, together with 55 exhibits. The main purpose of this declaration is to identify the exhibits (JFM 1 - JFM 55) which are referred to by the other declarant.
Michael John Hynes, Professor, Department of Genetics, University of Melbourne. There is a second declaration by this declarant which identifies a further 17 exhibits (MJH 1 - MJH 17).
The evidence in answer consists of statutory declarations from:
Albert J. J. van Ooyen, principal scientist at Gist-brocades Food Specialties R&D and one of the inventors of the invention, together with 4 exhibits (AVO 1 - AVO 4).
Joan Maree Kelly, Senior Lecturer, Department of Genetics, University of Adelaide together with 1 exhibit (JMK 1).
Evidence in reply consists of statutory declarations from:
John Francis McCann, as above, together with 6 exhibits (JFM 56 - JFM 61).
Ngaire Ann Pettit-Young, Senior Librarian, University of New South Wales.
Michael John Hynes, as above together with 3 exhibits (MJH 18 -MJH 20).
Peter Leonard Berquist, Deputy Vice Chancellor (Research) and Professor of Biology, Macquarie University, together with 7 exhibits (PLB 1 - PLB 7).
SECTION 40
Construction of Claim 1
The construction of claim 1 is important to a consideration of both the fair basis and the novelty of this claim so shall be considered in some detail.
1. A purified and isolated DNA sequence which encodes a polypeptide having the activity of the Aspergillus tubigensis XYL B enzyme, wherein the DNA sequence is selected from the group consisting of:
a) a DNA sequence of fungal origin as described in Figure 2;
b) genetic variants of the sequence of part a);
c) DNA sequences capable of hybridising to either one of the sequences of part a) and b), above
d) a DNA sequence which encodes a polypeptide as described in Figure 2.
e) a XYL B-encoding DNA sequence originating from Aspergillus tubigensis.
"A purified and isolated DNA sequence".
The opponent contends that this is beyond the scope of a recombinant DNA as described and includes purification and isolation of native sequences. While I agree with the opponent that this terminology is more usually seen in respect of proteins, I do not find that it is beyond the scope of the invention. Once the sequence has been disclosed then the DNA could be obtained by many well-known methods and once it is purified and isolated this would distinguish it from the naturally occurring DNA.
" which encodes a polypeptide having the activity of the Aspergillus tubigensis XYL B enzyme" The opponent contends this is not clear as the word "activity" is not defined in the specification. The opponent alleges that to give the term its ordinary meaning as used in the specification it means only the action of the enzyme which is equivalent to the activity of any endoxylanase. The applicant's evidence from the Kelly declaration at paragraph 16.1 states that XYL A, B and C will each have a specific activity which is distinctive. Paragraph 22.3 of the Kelly declaration states that with the characteristics disclosed in the specification of pH optima of 5.0 + 0.5, IEP of 4-4.3 and apparent molecular weight of 20-22 kDa, the activity of any endoxylanase could be compared against the activity of XYL B. The opponent's evidence, in the Berquist declaration, states (at paragraph 17 - 18) that the term enzyme activity refers to the rate at which an enzyme carries out the reaction it catalyses and should more correctly for purposes of comparison be represented as specific activity. Berquist further declares at paragraph 23 that features such as isoelectric point and molecular weight are coincidental to and/or independent of the activity of an enzyme. It appears to me from the evidence that while there is consensus as to the meaning of the term "specific activity" indicating both the action and reaction rate of the enzyme under specific conditions, the use of the term "activity" alone is not as clear. This is exemplified by the Kelly declaration, which at paragraph 14.9 states that "the DNA sequences and the polypeptides encoded thereby in claim 1 are based on that disclosed in figure 2. They will have a xylanase activity of varying degrees depending on the interaction of the encoded polypeptide with that of its substrate."
Hence I consider the phrase "a polypeptide having the activity of the Aspergillus tubigensis XYL B enzyme" as a polypeptide which has the same action (that is, it will catalyse the same chemical reaction) though not necessarily the same reaction rate (i.e. specific activity) as XYL B. Hence an enzyme must at least be an endoxylanase to have the same activity. The opponent urges that this alone is sufficient to fulfil the requirement of "having the same activity". However from the evidence (especially JFM 8: Wong et al, Multiplicity of b-1,4-Xylanases in Microorganisms: Functions and Applications, Microbiological Reviews, Sept.1988 p305-317) it appears that different endoxylanases may have different functions and operate on different substrates, that is they may catalyse different reactions. The determination of whether any particular endoxylanase does have the same activity as that of XYL B will therefore be a question of fact in any particular case, as the specification does not specifically disclose what this action is other than by describing it as an endoxylanase.
a) a DNA sequence of fungal origin as described in figure 2.
The opponent alleges this would include DNA sequences from fungal sources other than A. tubigensis and sequences that were less than the entire sequence described in Figure 2. While I agree that this does include DNA from fungal sources other than A. tubigensis, there is only one sequence disclosed in Figure 2. Figure 2 does not describe shorter sequences or any sequence variations, although the skilled addressee would know that there could be shorter sequences or minor variations to this sequence that would still result in an enzyme that had the activity of the XYL B enzyme. However I note that part b) of the claim defines just such genetic variants. Therefore it would appear to me that the applicant intended a literal interpretation of this phrase rather than a purposive one and I find that this part of the claim is limited to DNA sequences that are identical to that described in Figure 2 which arise from any fungal source.
b) genetic variants of the sequence of part a)
The opponents allege that this term is extremely broad and there is no definition of what is a genetic variant, there is only a list of things that it includes (at page 6 lines 18-21).
The applicant contends that the term "genetic variants" is clearly described on page 6 of the specification where it states at lines 14 - 21:
"Genetic variants include hybrid DNA sequences containing the XYL B-encoding sequence coupled to regulatory regions, such as promoter, secretion and terminator signals, originating from homologous or heterologous organisms. Genetic variants also include DNA sequences encoding the XYL B protein where the codon selection has been chosen for optimal recognition by the selected expression host."
The applicant cites Genetics Institute Inc v Kirin Amgen Inc (1998) 740 FCA (25 June 1998) where it states "it is well known that there is redundancy in the DNA coding for any particular amino acid and that one can make conservative substitutions for amino acids without making significant changes in the properties of the protein". The applicant also refers to the evidence of Kelly at paragraphs 14.1.2, 14.1.3 and 27 which states that she understands genetic variants to include not only sequences arising from the degeneracy of the genetic code but also "deletions, additions or substitutions of different nucleotide residues that result in sequences that encode the same or a functionally equivalent gene product. The gene product may contain deletions, additions or substitutions of amino acid residues within the sequence which results in a bioactive product."
There is nothing in the opponent's evidence to contradict the evidence of the applicant. While the term genetic variant may be broad I think that it is clear to the skilled addressee that it includes any variations of the DNA sequence which encodes a polypeptide having the activity (as earlier defined) of the A. tubigensis XYL B enzyme.
c) DNA sequences capable of hybridising to either one of the sequences of part a) and b), above
The opponents allege that the term "capable of hybridising" is not limited to the stringent conditions referred to in the body of the specification at page 6 lines 21 - 23 and page 7 lines 25 - 28. In the body of the specification where details of the invention are given, hybridisation is referred to in terms of hybridising under stringent conditions which are defined according to a protocol which equates to 66% homology according to opponent's evidence (Hynes, evidence in support paragraph 45) or 72% homology according to applicant's evidence (Kelly paragraph 28.1-28.6). In accordance with its plain meaning, I interpret the use of the term "hybridising" without reference to the stringent conditions in the claim, to include hybridising under any conditions and so it is not limited to any calculated homology. However this phrase is limited, as are all the sub-paragraphs of claim 1 to sequences which also encode a polypeptide having the activity (as earlier defined) of the A. tubigensis XYL B enzyme.
d) a DNA sequence which encodes a polypeptide as described in Figure 2.
The opponents allege this paragraph is not clear. However while it may not be clear why the applicant has chosen to include this paragraph when it is completely encompassed within the scope of paragraph b) above, I think that the plain meaning of the paragraph is clear. It is that it encodes any choice from among the degeneracy of the DNA code that results in the polypeptide of figure 2. As such it falls within the scope of the genetic variants above and does not add to the scope of the claim overall.
e) a XYL B-encoding DNA sequence originating from Aspergillus tubigensis.
The opponents allege that this paragraph is also unclear. I note that this is the only one of the paragraphs that is not linked in some way to the sequence disclosed in Figure 2. However it is limited to a sequence which originates from Aspergillus tubigensis. It is further limited to a "XYL B encoding DNA sequence". The phrase used here differs from that used earlier i.e. " DNA which encodes a polypeptide having the activity of the A. tubigensis XYL B enzyme". I construe this different use of terminology to imply that a different meaning was intended. Hence, this paragraph is limited to a DNA sequence which encodes an enzyme that is identical in function (both activity and reaction rate or specific activity) to the XYL B enzyme disclosed. Thus it might encompass minor variations from the disclosed enzyme but there must be substantial identity. Once again this paragraph falls within the scope of the genetic variants above and does not add to the scope of the claim overall.
Fair basis
The opponents contended that the claims are not fairly based because they are on the whole covetous and hence they are avoidably ambiguous. In Genetics Institute Inc v Kirin Amgen Inc 156 ALR 30 the issue of how broadly you can claim based on the disclosure of a specific sequence was discussed. At page 43 of the decision, Heerey J referred to the House of Lords decision in Biogen Inc v Medeva PLC [1997] RPC 1:
"On the other hand, if he has disclosed a beneficial property which is common to the class, he will be entitled to a patent for all products of that class (assuming them to be new) even though he has not made more than one or two of them."
He further referred to Biogen v Medeva at 44:
"It is not whether the claimed invention could deliver the goods, but whether the claims cover other ways in which they might be delivered: ways which owe nothing to the teaching of the patent or any principle which it disclosed."
Heerey J stated at page 46:
"The fundamental difference which distinguishes the present case from Biogen is that in the Amgen patent the coding sequence is disclosed. The patent thus discloses a "principle capable of general application" and discloses a beneficial property which is common to the class. It cannot be said of it that it "discloses no principle which would enable other products {of the class} to be made".
In the current case a coding sequence for Xylanase B is disclosed. This would form the basis for claiming a class of products which share the beneficial property of Xylanase B. Hence I find that all the claims are fairly based on the matter disclosed in the specification in this regard.
The opponent alleges that claims 2 - 8 are further not fairly based on the matter disclosed in the specification because in general terms there is no specific exemplification in the specification for the various constructs, transformed hosts, methods of expressing the polypeptide and the expressed polypeptide listed in these claims. The opponent alleges that there could be an undue burden of experimentation placed on the skilled addressee to work the invention. However this allegation is not supported by the opponent's own evidence. Hynes' declaration (evidence in support) at paragraph 116 cites many references that show that a skilled addressee would be able to clone and express a gene of interest and in particular xylanase genes in both homologous and heterologous hosts.
The opponents further allege that claims 2 and 6 are also not fairly based due to the use of the term "a polypeptide having xylanase activity" as this is broader in scope than the definition in claim 1 of a "a polypeptide having the activity of Aspergillus tubigensis XYL B enzyme". However as claims 2 and 6 are dependent on claim 1, I find this argument not persuasive. The term is necessarily limited by the fact that the polypeptide is produced using the DNA defined in claim 1.
Claim 10 is directed to "Purified and isolated expression and transcription regulatory regions as found in the 5' non-coding sequence of the Aspergillus tubigensis XYL B gene". The opponents allege that no such sequences are described in the specification and there is only a reference to two putative regions in Example 3.4.2. and that moreover if the "invention" is a new xylanase-encoding DNA sequence, then claim 10 does not define the invention.
The specification at page 25 (example 3.4.2) discloses that there is a 263 base pair (bp) 5' non-coding region. It further discloses putative TATA-boxes at 138-145 and 173-177. TATA-boxes are known to form part of the regulatory region of a gene. It further notes some repeated elements which are also found in the XYL A gene and another repeated sequence. The significance of these repeated sequences is not discussed. The applicant's evidence states (Kelly, paragraph 14.8) "that it would not be beyond the skills of the person skilled in the art to prove a region was a regulatory region by using mutation. Simply, if the regulatory region does not work it is likely to be pertinent to regulation." In response Hynes states at paragraph 40 "in my opinion, such a person would need to be aware of what mutations to introduce, and where, in the putative regulatory region (once this person has guessed that a particular region is regulatory) in order to make this (and no other portion of the DNA sequence) inoperative, and how to introduce such a mutation." However he does not state whether in his opinion this would be beyond the skill of the skilled addressee.
Neither declarant has discussed the relevance or significance of the repeated sequences and hence I am led to believe that they do not suggest themselves to be expression and/or transcription regulatory regions. The opponent alleges that it could take undue experimentation to determine such sequences. I tend to agree that as the only disclosure of regulatory regions within the 5' non-coding region is to two TATA-boxes, while it may not be beyond the skill of a person skilled in the art, it would require an undue burden of experimentation to further discover regions within the 5' non-coding region that are expression and transcription regulatory regions.
Hence I find that there is insufficient information in the specification to determine the "expression and transcription regulatory regions as found in the 5' non-coding sequence" as required by claim 10. The entire 263 bp sequence can be considered as an expression and regulatory region because it has been demonstrated to have this function. However the phrasing of the claim travels beyond a claim to the entire region per se and is hence not fairly based.
With regard to the argument that the claim to the regulatory region is not the same invention as the xylanase-encoding DNA sequence, I do not find this persuasive. The invention can be considered to be directed to a gene encoding a particular enzyme. It is well known that genes consist of regulatory (non-coding) regions and coding regions. To divide these up into separate inventions is to deny the singularity of the entity of the gene per se. If the gene per se is novel and inventive then the applicant should be entitled to claim both the coding regions and non-coding regions.
Claims 11 - 14 claim methods of using an enzyme encoded by the DNA sequence of any one of claims 1 to 3. It is not clear that an "enzyme encoded by the DNA" of the invention is limited to one that is produced as a result of working the invention i.e. one that is recombinantly expressed using the DNA of the invention. The naturally occurring enzyme, which the specification already admits is known in a purified and isolated state, is also "encoded" by the DNA sequence of the invention.
Similarly claims 16 - 17 claim bleaching sequences substantially as described in the specification with reference to example 5. It is not clear from the specification that example 5 uses the enzyme of the invention, that is the recombinantly expressed enzyme. It merely states at page 27 lines 22-23 that xylanase Endo II (= xylanase B) is used in the process.
As it is not clear that claims 11 -14 and 16 - 17 are limited to the enzyme of the invention (that is the enzyme when produced by the DNA of the invention) therefore these claims are not fairly based on the disclosures in the specification.
NOVELTY
At the hearing the opponent relied on 2 citations under the grounds of novelty:
A. Törrönen, R.L. Mach, R. Messner, R. Gonzalez, N. Kalkkinen, A. Harkki, and C Kubicek (1992), "The two major xylanases from Trichoderma reesei: characterisation of both enzymes and genes", Biotechnology vol. 10 pp. 1461 - 1465.
F. Shareck, C. Roy, M. Yaguchi, R. Morosoli, and D. Kluepfel (1991) "Sequences of three genes specifying xylanases in Streptomyces lividans", Gene 107: 75-82.
The generally accepted test for novelty is the "reverse infringement "test as set out in Meyers Taylor Pty Ltd v Vicarr Industries Ltd (1977) 137 CLR 228 at 235 where Aickin J stated:
"The basic test for want of novelty is the same as that for infringement and generally one can properly ask oneself whether the alleged anticipation would, if the patent were valid, constitute an infringement."
Infringement occurs where each and every one of the essential integers of the claim have been taken (Rodi and Wienenberger AG v Henry Showell Ltd (1960) RPC 367).
The first citation discloses the isolation, purification and sequences for the gene and protein for 2 xylanases from Trichoderma reesei. The xylanase II nucleotide sequence disclosed is 69% identical to the nucleotide sequence encoding the mature XYL B protein although the mature amino acid sequences are only 63% identical (JFM 59). In their evidence, the opponent calculated that under the conditions stated as "stringent hybridisation conditions" in the specification, nucleotide sequences with identity of 66% will hybridise. On the other hand the applicant's evidence showed it was necessary for there to be 72% homology for hybridisation to occur under the stringent conditions described. However as noted above the claim is not limited to stringent hybridisation conditions but to DNA sequences capable of hybridising to either the nucleotide sequence of XYL B or genetic variants thereof. I am satisfied that the opponent has shown that the xylanase II sequence disclosed in Törrönen is capable of hybridising to a sequence claimed in claim 1 of the application. However, I note that the opponent has not established that the sequence disclosed in Törrönen is capable of hybridisation under "stringent hybridisation conditions".
The xylanase II enzyme of Törrönen is described as an endoxylanase having isoelectric focusing point (IEP) of 9.0, a pH optimum of 4.5-5.5 and a molecular weight of 21 kD. This compares to Xylanase B which is an endoxylanase having pH optima of 5.0 + 0.5, IEP of 4-4.3 and apparent molecular weight of 20-22 kDa (Kelly paragraph 22.3). However, as noted above the molecular weight and IEP are considered to be coincidental to and/or independent of the activity of an enzyme. Thus the citation discloses an endoxylanase enzyme with an identical pH optimum. Further, the opponent's evidence in reply (second Hynes declaration at paragraphs 17 - 20 and JFM 46) asserts that due to the degree of homology and the degree of conservation around key areas, the A. tubigensis XYL B and the Törrönen xylanase II (and the Shareck xylanase C) enzymes all belong to the same class of enzymes, the G family endoxylanases. Nothing in the applicant's evidence indicated exactly what the action of XYL B is. The applicant made no submissions as to whether the action of these enzymes was in fact the same or different. I find that on the balance of probabilities Törrönen does disclose an enzyme that has the activity (as defined above) of the Aspergillus tubigensis XYL B enzyme described in the application. I do not believe that it has been shown that Törrönen discloses an enzyme with the "specific activity" of the Aspergillus tubigensis XYL B enzyme.
Hence the citation discloses each and every one of the integers required by claim 1. That is it discloses a purified and isolated DNA sequence which encodes a polypeptide having the activity of the A. tubigensis XYL B enzyme and the DNA sequence is capable of hybridising to the DNA sequence of fungal origin as described in Figure 2 of the application. Claim 1 does not place the limitations that the enzyme must have the "specific activity" of the A. tubigensis XYL B enzyme or that the hybridisation defined in part c) is under stringent conditions and, as such, is not novel in the light of Törrönen. Törrönen however does not disclose expression plasmids, their use, or methods of using the disclosed enzyme in bleaching sequences. Thus all of the remaining claims are novel in the light of this document.
Shareck discloses the sequences of 3 xylanase enzymes from Streptomyces lividans. The DNA sequence of xylanase C of Shareck has 66% homology to XYL B of the application and hence would be capable of hybridising to XYL B DNA. The xylanase C enzyme is described as an endoxylanase of molecular weight 20.7 kD. No information is given as to the pH optima although the temperature optima is stated to be 50-55 0C. No actual temperature optima is given for xylanase B in the application although I note that in the examples, the enzyme steps are carried out at 50 0C and 51 0C respectively and the applicant's evidence (Kelly paragraph 22.3) states that the temperature optimum is 50 0C. It is not clear if the citation discloses an enzyme which has the activity of A. tubigensis XYL B enzyme. As stated above the opponent's evidence shows that the A. tubigensis XYL B, the Törrönen xylanase II and the Shareck xylanase C enzymes all belong to the G family endoxylanases. Nothing in the applicant's submissions or evidence contradicted this. Therefore it seems more likely than not that all three of these enzymes do catalyse the same reaction.
Thus I believe on the balance of probabilities that xylanase C of S. lividans does have the activity (that is the same action though not necessarily the same reaction rate as defined above) as the xylanase B of the application. Hence, in the absence of reference to "specific activity", Claim 1 is not novel in the light of Shareck. Shareck also does not disclose expression plasmids, their use, or methods of using the disclosed enzyme in bleaching sequences. Hence all of the remaining claims are novel in the light of this document.
INVENTIVE STEP
The law on inventive step, as given in sections 7(2) and 7(3), makes it clear that obviousness is assessed against the common general knowledge alone or common general knowledge in combination with a document. Such a document must be publicly available and must reasonably be expected to have been ascertained, understood and regarded as relevant.
The legal test for obviousness is given in Wellcome Foundation Ltd v VR Laboratories (Aust) Pty Ltd (1981) 148 CLR 262 at 286
"What is important is that the patent itself should involve an inventive step, whether or not it is consciously taken by the patentee and whether or not it appeared obvious to the patentee himself. The test is whether the hypothetical addressee faced with the same problem would have taken as a matter of routine whatever steps might have led from the prior art to the invention, whether they are the steps of the inventor or not."
The applicant argued that there is no clear evidence that the hypothetical non-inventive person skilled in the art in Australia at the priority date, given the prior art, would as a matter of routine have taken the steps that the applicants took to arrive at the invention. However, I must consider what steps the skilled addressee would have taken, not what steps the applicant actually took to determine the DNA sequence. Both the opponent and the applicant urged that the test for inventiveness was not what the skilled addressee could try but what they would try. (Coopers Animal Health Australia Ltd v Western Stock DistributorsPty Ltd (1986) 6 IPR 545; WR Grace & Co v Asahi Kasei Kogyo KK, (1993) AIPC 90-974).
Genentech Inc. v The Wellcome Foundation (1988) 15 IPR 423, a decision of the UK court of appeal, discussed the standard of the skilled addressee in respect of a similar invention, the genetic engineering of Human tissue plasminogen activator. It found the skilled addressee in that case would be the team of highly qualified molecular biologists, protein sequencers, protein chemists and others. It further found that the hypothetical team should be credited with the best available equipment. In a decision of the office Genentech Inc and Another v Celtrix Pharmaceuticals Inc (1995) 34 IPR 162 in respect of a similar invention - the sequencing of BP53 - the hearing officer found, at 166, that the skilled addressee was "a molecular biologist skilled in recombinant technology used to manufacture DNA molecules". In this case I find the skilled addressee to be the same. I also find that the declarants for both the opponents and applicants, Hynes, Berquist, Kelly and Van Ooyen are skilled addressees. I note that Van Ooyen is also one of the inventors.
EP 463706
The prior art in this case includes the document EP 463706, also by the current applicant, which is referred to as prior art in the present specification. Example 1 of EP 463706 describes the purification and characterisation of Aspergillus tubigensis endo-xylanase XYL A. The crude extract was fractionated and the elution profile shown in Figure 2. Endo-xylanase activity was found in only peaks F and K, with peak K corresponding to XYL A and peak F being referred to as XYL 2 (now referred to as XYL B). EP 463706 further describes in detail a method for obtaining the DNA sequence for XYL A and overexpressing it in a host. It further discloses that such xylanases would be suitable for a range of applications including pulp bleaching. Thus, this document clearly identifies that one other endo-xylanase could be produced by Aspergillus tubigensis and that this enzyme may have additional useful properties, given its slightly higher iso-electric point than XYL A.
The applicant argued that, from reading EP 463706, there was no motivation to clone the XYL B gene. The second protein peak identified in EP 463706 may have been a proteolytic fragment of XYL A rather than a separate enzyme, in which case there would have been no motivation to clone the second peak enzyme. However, I do not accept this. While it is possible that XYL B could have been a proteolytic fragment, it was equally likely that it was a distinct enzyme. In any case, regardless of whether XYL B was a separate enzyme or a proteolytic fragment, I believe that the skilled addressee would have been motivated to isolate or clone it because of its useful properties as outlined above. I do not consider that the skilled addressee would have been deterred by the possibility that XYL B was in fact a fragment of XYL A.
The applicant also argued that even if there was motivation to clone the XYL B gene, there was a myriad of available cloning strategies and it would not have been possible to determine which strategy would work. The applicant referred to the decision of the Commissioner of Patents in Takeda Chemical Industries v F. Hoffman-La Roche Aktiengesellschaft (1996) APO3 (18 January 1996), where the hearing officer said in relation to the steps taken to purify a particular protein:
"In any case, I do not need to determine where there is an inventive step, the onus is on the opponent to prove there was not one. I do not believe that they have done so as they have not established that any particular method (or range of methods) from the commonly known techniques would have been obvious to use in purifying non-glycosylated human recombinant HPLC at the priority date of the claims. Therefore they have not shown that any of the claims lack inventive step."
In contrast to the Takeda decision, in this case there were a couple of techniques from the myriad of possibilities that the skilled worker would have been motivated to try. The first of these was to use the full-length probe of XYL A to see if this could hybridise to a XYL B gene. The applicant argued that this was not successful and it is only with hindsight that it is clear why this was so. However, although the applicant was unsuccessful, I do not accept that the person skilled in the art would necessarily expect the approach to work. They would have been aware that XYL B could be produced by a different gene and may not have been detected by heterologous hybridisation.
From this, I believe that the skilled addressee would have been directly led to clone the XYL B gene independently using the same approach as had been used to clone XYL A. That is, that the protein in peak F would have been purified, the N-terminal sequence obtained and a probe designed from that sequence. In my mind, this is not ex-post facto analysis, but a routine step by step elimination of one of the possible options before proceeding with the second option.
The applicant argued that the citation did not contain sufficient instruction to purify the protein. However, the applicant merely used the purification strategy of the citation and extracted the material from an SDS-page gel after electrophoresis. The opponent's evidence shows that approach to be a standard means of obtaining pure protein without further purification steps. I therefore believe that it does not provide any inventive step.
The applicant further argued that the strategy used to clone XYL A did not work for XYL B and that it was not evident where the problem lay.
At paragraph 13 of his declaration, Van Ooyen states:
"When cloning a gene such as XYL B, it is best to start with two partial amino acid sequences which are unambiguous and can be used to generate DNA probes with an acceptable degree of degeneracy. This was not the case with the sequences used for XYL B. The N-terminal sequence has to be determined twice and no internal sequence was available."
The two sequences determined showed ambiguities, indicating that the N-terminal sequence could be variable. From this, Van Ooyen submits that the design of the probe was "indeed very difficult and risky and required more than ordinary skill". He noted that the amino acids are such that a total of 512 combinations of DNA sequences encode them, which is a very high number and that most researchers would not be comfortable with such a high degree of degeneracy. Thus, the applicant contends that this design of the probe, which allowed the sequence to be determined, is inventive and non-routine.
However, at paragraph 77 of his evidence in reply, Hynes states:
"Before the claimed priority date, I would have expected that thorough work (but routine nonetheless) involving sufficient repeats of purifications, electrophoresis runs and N-terminus sequencing operations would have led to a satisfactory consensus sequence upon which to base a set of suitably degenerate oligonucleotide probes which could be successfully used to identify the portion of the gene coding for the N-terminus sequence of XYL B of A. tubigensis."
Thus, the opponent submits that the design of the probe was obvious, involving no more than routine experimentation. By repeating the sequencing sufficient times in order to obtain the consensus sequence, the degeneracy of the probe becomes significantly reduced and the number of possible DNA sequences become much less than the 512 noted by Van Ooyen. This appears to be exactly what the applicants did in the specification. I note also that the Kelly declaration, while indicating that "the N-terminal sequencing was not absolutely clear cut" and that a "consensus sequence for the N-terminal sequence was not immediately evident", does not give any indication that these problems required any more than routine experimentation.
The applicant claimed that the design of the probe was "risky" and that there was insufficient motivation for the skilled worker to try the approach. In my view, there is always an element of risk probing DNA libraries. I believe the skilled worker would minimise that risk by designing the best probe possible as the applicant has done. There was no evidence to suggest that they would have been taught away from designing this probe because of the high risk. The skilled worker need not be guaranteed of success, it only needs to be worthwhile to try.
Thus while the skilled addressee was not ensured of success at the outset, nonetheless he would have been led to try to sequence, clone and express the gene using the routine methodologies available to him. Similarly while he may have encountered difficulties along the way and may have needed to try several different approaches, these would not have prevented him from reaching his goal as they were all overcome in a routine manner. In this case, I believe that the opponent has established that the claims lack inventive step.
I find that the skilled addressee faced with the problem of how to obtain sufficient quantities of pure XYL B enzyme in Australia at the priority date would have been led to try to sequence, clone and express the DNA of XYL B using the techniques that were known in the art and would without the exercise of any inventive faculty have been able to overcome such difficulties as were faced during this process. Thus I find that there has been no invention in obtaining the DNA sequence for A. tubigensis XYL B in light of EP 463706.
As discussed under fair basis, the particular constructs, transformed hosts, methods of overexpressing the polypeptide and the polypeptide so expressed claimed in the dependent claims 2-7, 9, 10 and 15 are all obtainable using routine methods. There is no suggestion from the applicant of any inventiveness in any of these dependent claims. Hence I find that claims 2-7, 9, 10 and 15 also lack inventiveness.
Further the xylanase B enzyme per se is admitted as known and the process of using xylanases is also admitted prior art. Claims to a known process using a known enzyme, for purposes for which it is known that that type of enzyme would be suitable are also not inventive. Hence claims, 8,11-14, 16 and 17 to the use of the enzyme are also not inventive in light of the admitted prior art.
I find that the invention as claimed in all the claims does not involve an inventive step in the light of EP 463706.
Other documents
The opponent also submitted that the invention was obvious in light of the common general knowledge alone. However, I do not believe that the opponent has established this to be the case. There is no evidence to support the contention that the skilled person would be led to the invention claimed merely by combining aspects of common general knowledge. Since I have already found that the opponent has established lack of inventive step in the light of EP 463706 when combined with common general knowledge, I will give this no further consideration.
The opponent further asserted that the claims are not inventive in light of the common general knowledge plus either the Törrönen or Shareck documents cited above under novelty. These documents disclose endo-xylanases from Trichoderma reesei and Streptomyces lividans respectively, not Aspergillus tubigensis as described in the present specification. As discussed above, in the absence of the limitations that the enzyme must have the "specific activity" of the Aspergillus tubigensis XYL B enzyme and that the hybridisation is done under stringent conditions, present claim 1 may be considered to lack novelty in the light of both Törrönen and Shareck. However, if I were to consider claim 1 to include both these features, I do not believe that the skilled addressee reading either Törrönen or Shareck would be led, as a matter of routine, to the claimed invention. Thus, I do not consider either document to deprive claim 1 of inventive step and find similarly for all other claims.
Another point made by the opponent was that the Törrönen and Shareck documents disclose consensus sequences for the class of xylanases, which could be then used as probes to obtain and sequence the genes for all xylanases within the family. In his evidence in reply, Hynes makes a comparison between xylanases from different sources in which he determines that there is significant amino acid identity at the carboxy terminus of such enzymes. It is his view that it would have been obvious to a person skilled in the art, at or before the priority date of the claims, to prepare probes encoding the conserved portions of the carboxy terminus of XYL B and so arrive at the DNA sequence of XYL B.
On this point I agree with the applicant, that it is easy to do this exercise of comparing sequences once the sequence of XYL B is known. This seems to me to be applying ex post facto analysis in which the opponent has taken the known solution and worked backwards.
MANNER OF MANUFACTURE
The opponent argued, using NV Phillips Gloeilampenfabrieken v Mirabella International Pty Ltd (1995) 183 CLR 655 and Advanced Building Systems Pty Ltd v Ramset Fasteners (Aust) Pty Ltd (1998) 40 IPR 243 that section 18 of the Patents Act 1990 imposes a requirement for a threshold level of inventiveness for an invention to be a manner of manufacture.
While the opponent phrased their argument using the traditional language of manner of manufacture from Microcell, in my view, there is no difference in substance to the type of arguments already raised and considered under the ground of inventive step. It is particularly noted that the document relied on in inventive step is incorporated by reference into the specification. Under inventive step, it was argued that it was obvious to sequence, clone and express the DNA using known techniques. The same argument can simply be rephrased using the language of manner of manufacture. Thus, there has been no more that the application of known techniques to identify a DNA sequence known to exist, which encoded a known protein which had been at least partially described.
The opponent also submitted that the specification failed to attach any particular significance to methods of cloning and sequencing used and that this was an indication that there was no inventive step in these methods used. The opponent referred to the decision in Coopers v Western Stock Distributors (supra) where Wilcox J. held that it was "difficult to resist the inference that the failure of the inventors to emphasise their choice of DGBE in the applications……reflected their acceptance that there was nothing inventive about their choice." However, I do not believe that this is applicable to the present situation. The Coopers decision was concerned with fair basis of the specification on a provisional specification. This is not the issue here and it is well-established law that a specification does not have to point out the inventive step.
Having already considered the opponent's arguments under inventive step, I do not propose to consider them again under the ground of manner of manufacture.
CONCLUSION
I have found above that none of the claims are inventive in the light of EP 463706. While the design of the probe may have been difficult and risky, from the evidence before me I am convinced that this was achieved by no more than routine experimentation.
I have also found that claim 1, in so far as it does not define that the enzyme must have the "specific activity" of the Aspergillus tubigensis XYL B enzyme and that the hybridisation is done under stringent conditions, is not novel in the light of Törrönen and also Shareck.
I have further found that claims 10-14 and 16-17 are not fairly based on the matter disclosed in the specification.
Although the grounds of novelty and fair basis may be overcome by amendment, having regard to the subject matter to which the present application is directed, I do not discern anything disclosed in the specification as enabling it to be amended to overcome the ground of lack of inventive step.
As a result, I refuse the application.
COSTS
Costs normally follow the event and I see no reason to depart from this in this case. The opponent has been successful in their opposition and I award costs against the applicant.
Jodi Lawler
Delegate of the Commissioner of Patents
Patent attorneys for the applicant: Spruson and Ferguson
Patent attorneys for the opponent: Phillips Ormonde and Fitzpatrick
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