Summary

Mendel’s interest in transcription factors of Arabidopsis are clearly demonstrated in their patenting strategy.  Like Paradigm Genetics, Mendel’s early patent applications contain claims to large groups of sequences.  However, unlike Paradigm, Mendel’s patenting activities have extended beyond the initial bulk sequence claims.  A large and complex patent family has arrisen from a small number of initial patent applications.  Unlike Paradigm’s applications, the ‘927 application discussed above is the result of a series of continuations of previous applications.  The ‘927 application has itself led to still further continuation applications.  Many of the Mendel applications are still active, and even those that have abandoned or expired have led to further applications. Unlike Paradigm, Mendel has granted patents for some transcription factors and methods relating to transcription factors (e.g.US 6664446 , US 6835540, and US 6717034).

Mendel has invested significant resources in developing this patent document family. It is likely that Mendel will continue this strategy to eventually obtain patents on more transcription factors from Arabidopsis.  The language of the granted claims is crucial in determining whether claims over other dicot species will be possible.  The recent granted patent, US 6717034 (towards a transcription factor involved in modifying plant biomass), has the following claim language:

Claim #3: A transgenic plant comprising a recombinant polynucleotide comprising a polynucleotide sequence that hybridizes over its full length under stringent conditions to: (a) a nucleotide sequence comprising SEQ ID NO: 1, or a sequence that is fully complementary to the nucleotide sequence comprising SEQ ID NO: 1; or (b) a nucleotide sequence encoding a polypeptide comprising SEQ ID NO: 2, or a sequence that is fully complementary to the nucleotide sequence encoding a polypeptide comprising SEQ ID NO: 2; wherein the stringent conditions comprise wash conditions of 0.2×SSC to 2.0×SSC, 0.1% SDS at 60-65° C. and wherein expression of the polynucleotide sequence that hybridizes to either (a) or (b) increases the plant’s biomass as compared to a control plant not transformed with said recombinant polynucleotide.

Such language is more limiting in scope than that of the ‘927 patent.  However, it is not unreasonable to expect that such hybridization conditions may be met by at least homologs from other species within the mustard family. Whether-or-not homologs from other important crop species meet the same criteria cannot easily be deterimined, and would require experimental analysis. In part, this uncertainty evolves from the use of hybridization language in the claims.  Such claims, based on hybridization conditions, are difficult to quantify and the huge cost of possible litigation may act as a barrier to those interested in developing IP around transcription factors in other dicots.

To demonstrate the complexity of the patent document family that Mendel has created, consider the following diagram (the ‘927 application family):

(Hexagons: represent pending applications; Diamonds: represent adandoned or expired applications; F = filing date; CIP = continuation-in-part application)

Broad claims in Applications:
Arguebly, it is the role of a good patent attorney to provide the best possible outcome for a client.  It is probably for this reason that the scope of initial claims in a patent application is often as wide as possible.  Such broad intent is demonstrated in the text of the ‘927 application, where the following is stated:

Sequences homologous, i.e., that share significant sequence identity or similarity, to those provided in the Sequence Listing (except CBF sequences SEQ ID NOs: 1955-1960), derived from Arabidopsis thaliana or from other plants of choice, are also an aspect of the invention. Homologous sequences can be derived from any plant including monocots and dicots and in particular agriculturally important plant species, including but not limited to, crops such as soybean, wheat, corn (maize), potato, cotton, rice, rape, oilseed rape (including canola), sunflower, alfalfa, clover, sugarcane, and turf; or fruits and vegetables, such as banana, blackberry, blueberry, strawberry, and raspberry, cantaloupe, carrot, cauliflower, coffee, cucumber, eggplant, grapes, honeydew, lettuce, mango, melon, onion, papaya, peas, peppers, pineapple, pumpkin, spinach, squash, sweet corn, tobacco, tomato, tomatillo, watermelon, rosaceous fruits (such as apple, peach, pear, cherry and plum) and vegetable brassicas (such as broccoli, cabbage, cauliflower, Brussels sprouts, and kohlrabi). Other crops, including fruits and vegetables, whose phenotype can be changed and which comprise homologous sequences include barley; rye; millet; sorghum; currant; avocado; citrus fruits such as oranges, lemons, grapefruit and tangerines, artichoke, cherries; nuts such as the walnut and peanut; endive; leek; roots such as arrowroot, beet, cassaya, turnip, radish, yam, and sweet potato; and beans. The homologous sequences may also be derived from woody species, such pine, poplar and eucalyptus, or mint or other labiates. In addition, homologous sequences may be derived from plants that are evolutionarily-related to crop plants, but which may not have yet been used as crop plants. Examples include deadly nightshade (Atropa belladona), related to tomato; jimson weed (Datura strommium), related to peyote; and teosinte (Zea species), related to corn (maize).

The importance of using hybridisation and sequence similarity language to broaden the scope of claims can be inferred from the following two figures from the ‘927 application.  These figures relate the evolutionary position of Arabidopsis to other important crops.  One may suspect that those crops most closely related to Arabidopsis would be most likely to have genes with highly homologous sequences (and thus satisfy the hybridisation and/or similarity ranges stated in the claims):