Analysis of Patenting “Hot Spots”
Analysis of Patenting “Hot Spots” on the Arabidopsis genome map
During the mapping of patent documents to the corresponding regions of the Arabidopsis map it was noticed that there are a number of places on the map that have a higher-than-average patenting activity.
These regions included:
| Arabidopsis Chromosome |
Map Position (Mbases) |
Number of Patents | Number of Sequences Mapped to the region |
|---|---|---|---|
|
2 |
3.6 |
6 |
7 |
|
3 |
3.6 |
10 |
14 |
|
3 |
13.5 |
7 |
78 |
|
4 |
12.9 |
8 |
10 |
From this table further analyses revealed the following:
Arabidopsis Chromosome 3 and the 47-patent hot spot at Map position 13.5Mb:
Analysis of the sequences from these 47 patents (by BLAST at NCBI) demonstrated that a ~450bp fragment from a cloning vector contaminates the chromosome sequence at this position. The large number of patent documents matching at this site are a result of matches with this region from patent sequences unrelated to Arabidopsis sequences. Our method is sensitive to such “contamination” since it relies on almost identical matches with the chromosomal sequences of Arabidopsis to identify patented sequences (and hence patents of interest from Arabidopsis). It is interesting that this sequence contamination has persisted in the Arabidopsis genome sequence and suggests that the methods used to screen for vector contamination are not entirely reliable.
Arabidopsis Chromosome 3: The 10-patent-hot-spot at Map position 3.6Mb:
US patents appearing at this hotspot include those listed in the following table:
| Patent Number |
Issue Date | Title (use/description of sequence claimed) |
Status | Applicant |
|---|---|---|---|---|
| 5912415 | 06-15-1999 | Arabidopsis spindly gene, methods of identification and use (gene involved in the gibberellin signal transduction) |
Expired | Regents of the University of Minnesota |
| 5965793 | 10-12-1999 | Strong early seed-specific gene regulatory region (seed-specific expression/modifying fatty acid production in seed tissue) |
In force | Monsanto Company, Inc |
| 6291742 | 09-18-2001 | Production of hydroxylated fatty acids in genetically modified plants (plant fatty acyl hydroxylases) |
In force | Carnegie Institution of Washington, Monsanto Company Inc. |
| 6310194 | 10-30-2001 | Plant fatty acid hydroxylases (plant fatty acyl hydroxylases) |
In force | Carnegie Institution of Washington, Monsanto Company Inc. |
| 6342658 | 01-29-2002 | Fatty acid desaturases and mutant sequences thereof (Brassica: mutation in a delta-12 or delta-15 fatty acid desaturase gene) |
In force | Cargill, Inc |
| 6372965 | 04-16-2002 | Genes for microsomal delta-12 fatty acid desaturases and hydroxylases from plants (alteration of plant lipid composition) |
In force | E.I. du Pont de Nemours and Co |
| 6642436 | 11-04-2003 | DNA encoding for plant digalactosyldiacylglycerol galactosyltransferase and methods of use (Arabidopsis: cDNA encoding digalactosyldiacylglycerol galactosyltransferase (DGD1)) |
In force | Board of Trustees operating Michigan State University |
| 6872872 | 03-29-2005 | Genes for microsomal delta-12 fatty acid desaturases and related enzymes from plants (Arabidopsis thaliana cDNA for microsomal delta-12 desaturase) |
In force | E. I. du Pont de Nemours and Co |
| 6919466 | 07-19-2005 | Genes for microsomal delta-12 fatty acid desaturases and related enzymes from plants (use of fatty acid desaturase enzymes to modify plant lipid composition) |
In force | E. I. du Pont de Nemours and Co |
| 6967243 | 11-22-2005 | Fatty acid desaturases and mutant sequences thereof (Brassicaceae: plants having at least one mutation that controls levels of unsaturated fatty acids) |
In force | Cargill, Inc |
Essentially this hotspot refers to (amongst others) claims against fatty acid desaturase (FAD) genes from Arabidopsis and related organisms such as Brassica spp. Some of the sequences mapping to chromosome 3 of Arabidopsis are in fact the FAD gene from rape (Brassica napus). The importance of FAD claims is underlined by the presence of large private companies involved in agritech research and development: Monsanto, Du Pont, and Cargill. Manipulation of FAD levels in plants is one way in which the ratio of saturated to unsaturated oils might be controlled. Such manipulation is of interest due to the human health implications and industrial applications (including biodiesel) possible through the generation of crop plants with modified levels of unsaturated oils. The patents listed above are an example of a small patent thicket that has arisen around an industrially-important gene family (in this case FAD from Arabidopsis and Brassica sp.). Although beyond the scope of the present landscape: It is interesting to speculate that the FAD genes from other species (e.g. Gossypium hirsutum) may also be the focus of patenting activity.
Arabidopsis Chromosome 2 and the 6-patent hot spot at Map position 3.6Mb:
US patents appearing at this hotspot include those listed in the following table:
| Patent Number |
Issue Date | Title (use/description of sequence claimed) |
Status | Applicant |
|---|---|---|---|---|
| 6316004 | 11-13-2001 | Chimeric somatostatin containing protein and encoding DNA, plasmids of expression, method for preparing chimeric protein, strain-producers, immunogenic composition, method for increasing the productivity of farm animals |
Expired | Tikhonenko; T. |
| 6372457 | 04-16-2002 | Process and materials for production of glucosamine (contains sequence from many expression vectors) |
In force | Arkion Life Sciences LLC |
| 6537777 | 03-25-2003 | Human porphobilinogen deaminase sequences | In force | Hemebiotech A/S |
| 6667150 | 12-23-2003 | Method and phage for the identification of nucleic acid sequences encoding members of a multimeric (poly) peptide complex | In force | Morphosys AG |
| 6933146 | 08-23-2005 | Methods and means for producing efficient silencing construct using recombinational cloning | In force | Commonwealth Scientific and Industrial Research Corporation; |
| 6972197 | 12-06-2005 | Plant chromosome compositions and methods (SEQ ID NO 4: Unknown, expressed Arabidopsis protein. centromeric sequence?) |
In force | The University of Chicago |
Again, most of the patenst above do not deal with direct claims to sequences from Arabidopsis or other plants. Instead there appears to be some vector contamination in the chr2 sequence from Arabidopsis, and this appears to account for much of the “hotspot” activity here.
Arabidopsis Chromosome 4 and the 8-patent hot spot at Map position 12.9Mb:
US patents appearing at this hotspot include those listed in the following table:
| Patent Number |
Issue Date | Title (use/description of sequence claimed) |
Status | Applicant |
|---|---|---|---|---|
| 5856452 | 01-05-1999 | Oil bodies and associated proteins as affinity matrices (Oleosin from Arabidopsis thaliana) |
In force | Sembiosys Genetics Inc |
| 5891859 | 04-06-1999 | Method for regulating cold and dehydration regulatory genes in a plant (Method defined by part of the CBF1 gene from Arabidopsis) |
In force | Michigan State University |
| 5892009 | 04-06-1999 | DNA and encoded protein which regulates cold and dehydration regulated genes (The CBF1 gene from Arabidopsis) |
In force | Michigan State University |
| 6198021 | 03-06-2001 | GA 20-oxidase gene sequences (Transgenic plants with GA 20-oxidase from Arabidopsis) |
In force | Long Ashton Research Station |
| 6417428 | 07-09-2002 | Plant having altered environmental stress tolerance (transcription factors from Arabidopsis) |
In force | Michigan State University/Mendel Biotechnology Inc. |
| 6495742 | 12-17-2002 | Genes encoding plant transcription factors (Transcription factor from Arabidopsis) |
In force | Independent Administrative Institute Japan International Research Center for Agricultural Sciences |
| 6670528 | 12-30-2003 | Environmental stress-tolerant plants (Arabidopsis thaliana DREB1A transcription factor) |
In force | Independent Administrative Institute, Japan International Research Center for Agricultural Sciences |
| 6706866 | 03-16-2004 | Plant having altered environmental stress tolerance (Transcription factor from Arabidopsis) |
In force | Michigan State University |
(Note that the Applicant in the above tables was that listed in the PatentLens database entry for the given patent. Where no company name appeared (only inventors names) a further USPTO search was conducted to identify assignee information. Note: These assignments may not be accurate after the date of issue.)