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.)