T 2354/09 – A Tree In The Woods

This is an appeal against the rejection of the opposition against the patent under consideration.

Claim 1 as granted read:

1. An L-amino acid producing bacterium belonging to the genus Escherichia, wherein the bacterium has been modified so that the L-amino acid production by said bacterium is enhanced by enhancing activities of proteins as defined in the following (E) or (F) in a cell of said bacterium:

(E) a protein which comprises the amino acid sequence shown in SEQ ID NO:11 in Sequence listing;

(F) a protein which comprises an amino acid sequence including deletion, substitution, insertion or addition of 1-22 amino acids in the amino acid sequence shown in SEQ ID NO:11 in Sequence listing, and which has an activity of making bacterium having enhanced resistance to L-amino acids and/or its analogs;

the activities of proteins being enhanced by transformation of said bacterium with DNA coding for protein as defined in (E) or (F), or by alteration of promoter sequence of said DNA on the chromosome of the bacterium.

Among other things, the opponent pointed out that this claim was lacking novelty. The production of L-amino acids was an inherent property of E. coli bacteria. Document D1 disclosed the complete E. coli K-12 genome which included the b1242 gene (SEQ ID NO:11) encoding a protein as defined in part (E) of claim 1. Document D1 referred to the high redundancy of the sequencing strategy and to subclones with genome fragments of a size (15 to 20 kb; 250 kb) greater than that of the b1242 gene. Thus, following this sequencing strategy, it was inevitable to obtain subclones containing the complete b1242 gene. When cloning the E. coli K-12 genome, the number of copies of the b1242 gene as well as those of other genes, was increased and thus, the E. coli bacterium of claim 1 was inherently obtained.

The Board rejected this argument:

[15] Document D1, the sole document discussed in the decision under appeal in the context of novelty […], discloses the complete genome of E. coli K-12. The appellant argues that, by determining this sequence, an E. coli bacterium as defined in the claims would have been “inherently” produced […].

[16] The genome of E. coli K-12 disclosed in document D1 is obtained by a combination of three different approaches. The first 1.92 Mb (positions 2,686,777 to 4,639,221 in base pairs) are sequenced from an overlapping set of 15 to 20 kb MG1655 lambda clones, a second segment (2,475,719 to 2,690,160) is sequenced using non-overlapping DNA fragments by a popout plasmid approach, and the largest portion of the genome (22,551 to 2,497,976) is sequenced from M13 Janus shotguns with fragments of about 250 kb. The M13 Janus shotgun strategy involves an initial random sequencing at a four to fivefold redundancy and it is the most efficient strategy […]. There is, however, no information either in document D1 or in any other document on file on the precise location of the b1242 gene within the E. coli K-12 genome and thus, it cannot be excluded with certainty that the b1242 gene is located within the second segment of the E. coli genome in which non-overlapping fragments were used.

[17] Similarly, with the evidence at hand, it cannot be said with certainty that the complete, full-length sequence of the b1242 gene is inevitably present in at least one of the clones or subclones resulting from the three cloning strategies used in document D1. There is no evidence on file of the presence of a clone containing and identifying the specific sequence of the b1242 gene (SEQ ID NO:11). There is also no evidence on file that any of the clones or subclones obtained by the strategies used in document D1 results in an E. coli bacterium having an enhanced production of L-amino acids.

[18] Moreover, according to the established case law (cf. inter alia T 18/09 [10-15]), the presence of a cDNA sequence - without any further (indexed) information or identification - in a clone collection, a sequence databank or, as in the present case, in a complete genome sequence of about 4.64 Mb, does not “make available” this cDNA sequence directly and unambiguously to the skilled person. This is in line with the difference made in the case law between an “implicit” and an “inherent” disclosure as laid down in the decision G 2/88.

[19] Thus, the board considers the claimed subject-matter to fulfil the requirements of A 54.

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