Mendel Biotechnology Patents

Patent applications for Arabidopsis bulk sequences made by Mendel Biotechnology Inc.

The following is an example of one of the 11 patent documents identified as belonging to Mendel Biotechnology Inc.  The ‘927 application is discussed here for the following reasons:

  • It involves a large group of Arabidopsis sequences (i.e. a bulk sequence claim),
  • deals with a specific class of target sequences that are likely to have numerous applications across many flowering plant species (of interest to many), and
  • demonstrates Mendel’s stated strategy of targeting transcription factors (TFs) from Arabidopsis (strategic IP?)

(Note that this patent application contains by far the most sequence claims compared to other applications.  Note also that there are ~1800 TFs in the Arabidopsis genome and there are >1900 SEQ IDs listed in this application alone! Hence this application is likely to be a significant patent application with respect to TFs for many plant species.)

Patent or Publication No. Title, Independent Claims and Summary Applicant
US 2004/0019927 A1

  • Earliest priority – 18 Apr 2001
  • Filed – 25 Feb 2003
  • Granted –
  • Expected expiry –

THIS IS NOT A GRANTED
PATENT

Title – Polynucleotides and polypeptides in plants

Claim 1
A transgenic plant comprising a recombinant polynucleotide having a polynucleotide sequence, or a complementary polynucleotide sequence thereof, selected from the group consisting of:
(a) a polynucleotide sequence encoding a polypeptide, wherein said polypeptide is selected from the group consisting of SEQ ID NO: 2N, wherein N=1-229, SEQ ID NO: 467; 488-490; 501-503; 505; 512-515; 521-522; 525-526; 528; 530; 534-537; 540; 558-559; 569; 587-594; 597; 607-609; 621-626; 635-639; 665-669; 708-713; 720-721; 736-739; 742; 780-807; 824; 835-837; 851-854; 865-867; 890-891; 903-907; 910-913; 922-923; 926; 933-934; 943; 953-960; 966-967; 987-988;994; 1011; 1035-1042; 1064-1073; 1081-1090; 1105-1110; 1122; 1129-1133; 1139-1141; 1157-1158; 1176-1186; 1191; 1200-1201; 1221-1248; 1254-1257; 1263; 1270; 1288-1291; 1302; 1310-1314; 1324-1327; 1338-1339; 1342-1343; 1362-1364; 1378; 1391-1392; 1395; 1399-1418; 1433; 1453-1454; 1457-1459; 1466-1467; 1492-1498; 1500-1501; 1503-1504; 1522; 1528; 1533-1535; 1540-1541; 1563-1566; 1572; 1583-1586; 1593-1594; 1621-1624; 1645-1646; 1655-1658; 1670; 1674; 1681; 1687; 1701-1705; 1710-1713; 1727; 1735-1737; 1743; 1754-1756; 1761-1762; 1765; 1769; 1781; 1785; 1790; 1805; 1813; 1838-1846; 1857; 1863; 1874-1875; 1883-1884; 1897-1901; 1911-1912; 1917-1920; 1929-1930; 1937-1939; 1942-1943; and SEQ ID NO: 2N, wherein N=974-1101;
(b) a polynucleotide sequence encoding a polypeptide, wherein said polynucleotide sequence is selected from the group consisting of SEQ ID NO: 2N-1, wherein N=1-229, SEQ ID NO: 459-466;468-487; 491-500; 504; 506-511; 516-520; 523-524; 527; 529; 531-533; 538-539; 541-557; 560-568; 570-586; 595-596; 598-606; 610-620; 627-634; 640-664; 670-707; 714-719; 722-735; 740-741; 743-779; 808-823; 825-834; 838-850; 855-864; 868-889; 892-902; 908-909; 914-921; 924-925; 927-932; 935-942; 944-952; 961-965; 968-986; 989-993; 995-1010; 1012-1034; 1043-1063; 1074-1080; 1091-1104; 1111-1121; 1123-1128; 1134-1138; 1142-1156; 1159-1175; 1187-1190; 1192-1199; 1202-1220; 1249-1253; 1258-1262; 1264-1269; 1271-1287; 1292-1301; 1303-1309; 1315-1323; 1328-1337; 1340-1341; 1344-1361; 1365-1377; 1379-1390; 1393-1394; 1396-1398; 1419-1432; 1434-1452; 1455-1456; 1460-1465; 1468-1491; 1499; 1502; 1505-1521; 1523-1527; 1529-1532; 1536-1539; 1542-1562; 1567-1571; 1573-1582; 1587-1592; 1595-1620; 1625-1644; 1647-1654; 1659-1669; 1671-1673; 1675-1680; 1682-1686; 1688-1700; 1706-1709; 1714-1726; 1728-1734; 1738-1742; 1744-1753; 1757-1760; 1763-1764; 1766-1768; 1770-1780; 1782-1784; 1786-1789; 1791-1804; 1806-1812; 1814-1837; 1847-1856; 1858-1862; 1864-1873; 1876-1882; 1885-1896; 1902-1910; 1913-1916; 1921-1928; 1931-1936; 1940-1941; 1944-1946, and SEQ ID NO: 2N-1, wherein N=974-1101;
(c) a polynucleotide sequence encoding the polypeptide sequence of (a) with conservative substitutions as defined in Table 2, wherein said polypeptide sequence of (a) with conservative substitutions is a transcription factor;
(d) a variant of the polynucleotide sequences of (a) or (b), which is at least 80% identical to a sequence of (a) or (b), and wherein said sequence variant encodes a polypeptide that is a transcription factor;
(e) an orthologous sequence of the polynucleotide sequences of (a) or (b), which is at least 80% identical to a sequence of (a) or (b), and wherein said orthologous sequence encodes a polypeptide;
(f) a paralogous sequence of the polynucleotide sequences of (a) or (b), which is at least 80% identical to a sequence of (a) or (b), and wherein said paralogous sequence encodes a polypeptide;
(g) a polynucleotide sequence encoding a polypeptide comprising a conserved domain that exhibits at least 80% sequence homology with the conserved domain of the polypeptide of (a), wherein said polypeptide comprising a conserved domain of a transcription factor; and wherein said conserved domain of (a) is bounded by amino acid residue coordinates according to Table 5; and
(h) a polynucleotide that hybridizes to the polynucleotide of (a) or (b) under stringent conditions.
Claim 92
An expression cassette comprising:
(1) a constitutive, inducible, or tissue-specific promoter; and
(2) a recombinant polynucleotide having a polynucleotide sequence, or a complementary polynucleotide sequence thereof, selected from the group consisting of:
(a) a polynucleotide sequence encoding a polypeptide, wherein said polypeptide is selected from the group consisting of SEQ ID NO: 2N, wherein N=1-229, SEQ ID NO: 467; 488-490; 501-503; 505; 512-515; 521-522; 525-526; 528; 530; 534-537; 540; 558-559; 569; 587-594; 597; 607-609; 621-626; 635-639; 665-669; 708-713; 720-721; 736-739; 742; 780-807; 824; 835-837; 851-854; 865-867; 890-891; 903-907; 910-913; 922-923; 926; 933-934; 943; 953-960; 966-967;987-988;994; 1011; 1035-1042; 1064-1073; 1081-1090; 1105-1110; 1122; 1129-1133; 1139-1141; 1157-1158; 1176-1186; 1191; 1200-1201; 1221-1248; 1254-1257; 1263; 1270; 1288-1291; 1302; 1310-1314; 1324-1327; 1338-1339; 1342-1343; 1362-1364; 1378; 1391-1392; 1395; 1399-1418; 1433; 1453-1454; 1457-1459; 1466-1467; 1492-1498; 1500-1501; 1503-1504; 1522; 1528; 1533-1535; 1540-1541; 1563-1566; 1572; 1583-1586; 1593-1594; 1621-1624; 1645-1646; 1655-1658; 1670; 1674; 1681; 1687; 1701-1705; 1710-1713; 1727; 1735-1737; 1743; 1754-1756; 1761-1762; 1765; 1769; 1781; 1785; 1790; 1805; 1813; 1838-1846; 1857; 1863; 1874-1875; 1883-1884; 1897-1901; 1911-1912; 1917-1920; 1929-1930; 1937-1939; 1942-1943; and SEQ ID NO: 2N, wherein N=974-1101;
(b) a polynucleotide sequence encoding a polypeptide, wherein said polynucleotide sequence is selected from the group consisting of SEQ ID NO: 2N-1, wherein N=1-229, SEQ ID NO: 459-466; 468-487; 491-500; 504; 506-511; 516-520; 523-524; 527; 529; 531-533; 538-539; 541-557; 560-568; 570-586; 595-596; 598-606; 610-620; 627-634; 640-664; 670-707; 714-719; 722-735; 740-741; 743-779; 808-823; 825-834; 838-850; 855-864; 868-889; 892-902; 908-909; 914-921; 924-925; 927-932; 935-942; 944-952; 961-965; 968-986; 989-993; 995-1010; 1012-1034; 1043-1063; 1074-1080; 1091-1104; 1111-1121; 1123-1128; 1134-1138; 1142-1156; 1159-1175; 1187-1190; 1192-1199; 1202-1220; 1249-1253; 1258-1262; 1264-1269; 1271-1287; 1292-1301; 1303-1309; 1315-1323; 1328-1337; 1340-1341; 1344-1361; 1365-1377; 1379-1390; 1393-1394; 1396-1398; 1419-1432; 1434-1452; 1455-1456; 1460-1465; 1468-1491; 1499; 1502; 1505-1521; 1523-1527; 1529-1532; 1536-1539; 1542-1562; 1567-1571; 1573-1582; 1587-1592; 1595-1620; 1625-1644; 1647-1654; 1659-1669; 1671-1673; 1675-1680; 1682-1686; 1688-1700; 1706-1709; 1714-1726; 1728-1734; 1738-1742; 1744-1753; 1757-1760; 1763-1764; 1766-1768; 1770-1780; 1782-1784; 1786-1789; 1791-1804; 1806-1812; 1814-1837; 1847-1856; 1858-1862; 1864-1873; 1876-1882; 1885-1896; 1902-1910; 1913-1916; 1921-1928; 1931-1936; 1940-1941; 1944-1946, and SEQ ID NO: 2N-1, wherein N=974-1101;
(c) a polynucleotide sequence encoding the polypeptide sequence of (a) with conservative substitutions as defined in Table 2, wherein said polypeptide sequence of (a) with conservative substitutions is a transcription factor;
(d) a variant of the polynucleotide sequences of (a) or (b), which is at least 80% identical to a sequence of (a) or (b), and wherein said sequence variant encodes a polypeptide that is a transcription factor;
(e) an orthologous sequence of the polynucleotide sequences of (a) or (b), which is at least 80% identical to a sequence of (a) or (b), and wherein said orthologous sequence encodes a polypeptide that is a transcription factor;
(f) a paralogous sequence of the polynucleotide sequences of (a) or (b), which is at least 80% identical to a sequence of (a) or (b), and wherein said paralogous sequence encodes a polypeptide that is a transcription factor;
(g) a polynucleotide sequence encoding a polypeptide comprising a conserved domain that exhibits at least 80% sequence homology with the conserved domain of the polypeptide of (a), wherein said polypeptide comprising a conserved domain of a transcription factor; and wherein said conserved domain of (a) is bounded by amino acid residue coordinates according to Table 5; and
(h) a polynucleotide that hybridizes to the polynucleotide of (a) or (b) under stringent conditions; wherein said recombinant polynucleotide is operably linked to said promoter.
Claim 94
 A method for producing a modified plant having a modified trait, the method comprising:
(a) selecting a polynucleotide that encodes a polypeptide, wherein said polynucleotide has a sequence, or a complementary sequence thereof, selected from the group consisting of:
(i) a polynucleotide sequence encoding a polypeptide, wherein said polypeptide is selected from the group consisting of SEQ ID NO: 2N, wherein N=1-229, SEQ ID NO: 467; 488-490; 501-503; 505; 512-515; 521-522; 525-526; 528; 530; 534-537; 540; 558-559; 569; 587-594; 597; 607-609; 621-626; 635-639; 665-669; 708-713; 720-721; 736-739; 742; 780-807; 824; 835-837; 851-854; 865-867; 890-891; 903-907; 910-913; 922-923; 926; 933-934; 943; 953-960; 966-967; 987-988; 994; 1011; 1035-1042; 1064-1073; 1081-1090; 1105-1110; 1122; 1129-1133; 1139-1141; 1157-1158; 1176-1186; 1191; 1200-1201; 1221-1248; 1254-1257; 1263; 1270; 1288-1291; 1302; 1310-1314; 1324-1327; 1338-1339; 1342-1343; 1362-1364; 1378; 1391-1392; 1395; 1399-1418; 1433; 1453-1454; 1457-1459; 1466-1467; 1492-1498; 1500-1501; 1503-1504; 1522; 1528; 1533-1535; 1540-1541; 1563-1566; 1572; 1583-1586; 1593-1594; 1621-1624; 1645-1646; 1655-1658; 1670; 1674; 1681; 1687; 1701-1705; 1710-1713; 1727; 1735-1737; 1743; 1754-1756; 1761-1762; 1765; 1769; 1781; 1785; 1790; 1805; 1813; 1838-1846; 1857; 1863; 1874-1875; 1883-1884; 1897-1901; 1911-1912; 1917-1920; 1929-1930; 1937-1939; 1942-1943; and SEQ ID NO: 2N, wherein N=974-1101;
(ii) a polynucleotide sequence encoding a polypeptide, wherein said polynucleotide sequence is selected from the group consisting of SEQ ID NO: 2N-1, wherein N=1-229, SEQ ID NO: 459-466; 468-487; 491-500; 504; 506-511; 516-520; 523-524; 527; 529; 531-533; 538-539; 541-557; 560-568; 570-586; 595-596; 598-606; 610-620; 627-634; 640-664; 670-707; 714-719; 722-735; 740-741; 743-779; 808-823; 825-834; 838-850; 855-864; 868-889; 892-902; 908-909; 914-921; 924-925; 927-932; 935-942; 944-952; 961-965; 968-986; 989-993; 995-1010; 1012-1034; 1043-1063; 1074-1080; 1091-1104; 1111-1121; 1123-1128; 1134-1138; 1142-1156; 1159-1175; 1187-1190; 1192-1199; 1202-1220; 1249-1253; 1258-1262; 1264-1269; 1271-1287; 1292-1301; 1303-1309; 1315-1323; 1328-1337; 1340-1341; 1344-1361; 1365-1377; 1379-1390; 1393-1394; 1396-1398; 1419-1432; 1434-1452; 1455-1456; 1460-1465; 1468-1491; 1499; 1502; 1505-1521; 1523-1527; 1529-1532; 1536-1539; 1542-1562; 1567-1571; 1573-1582; 1587-1592; 1595-1620; 1625-1644; 1647-1654; 1659-1669; 1671-1673; 1675-1680; 1682-1686; 1688-1700; 1706-1709; 1714-1726; 1728-1734; 1738-1742; 1744-1753; 1757-1760; 1763-1764; 1766-1768; 1770-1780; 1782-1784; 1786-1789; 1791-1804; 1806-1812; 1814-1837; 1847-1856; 1858-1862; 1864-1873; 1876-1882; 1885-1896; 1902-1910; 1913-1916; 1921-1928; 1931-1936; 1940-1941; 1944-1946, and SEQ ID NO: 2N-1, wherein N=974-1101;
(iii) a polynucleotide sequence encoding the polypeptide sequence of (i) with conservative substitutions as defined in Table 2, wherein said polypeptide sequence of (i) with conservative substitutions is a transcription factor;
(iv) a variant of the polynucleotide sequences of (a) or (b), which is at least 80% identical to a sequence of (i) or (ii), and wherein said sequence variant encodes a polypeptide that is a transcription factor;
(v) an orthologous sequence of the polynucleotide sequences of (i) or (ii), which is at least 80% identical to a sequence of (i) or (ii), and wherein said orthologous sequence encodes a polypeptide that is a transcription factor;
(vi) a paralogous sequence of the polynucleotide sequences of (i) or (ii), which is at least 80% identical to a sequence of (i) or (ii), and wherein said paralogous sequence encodes a polypeptide that is a transcription factor;
(vii) a polynucleotide sequence encoding a polypeptide comprising a conserved domain that exhibits at least 80% sequence homology with the conserved domain of the polypeptide of (i), wherein said polypeptide comprising a conserved domain of a transcription factor; and wherein said conserved domain of (i) is bounded by amino acid residue coordinates according to Table 5, and
(viii) a polynucleotide that hybridizes to the polynucleotide of (i) or (ii) under stringent conditions;
(b) inserting the polynucleotide into an expression cassette according to claim 92;
(c) introducing the expression cassette into a plant or a cell of a plant to overexpress the polypeptide, thereby producing said modified plant; and (d) selecting said modified plant having said modified trait.

The claims are generally drawn to:

  • A transgenic plant comprising a recombinant polynucleotide having a sequence, or a complementary sequence thereof, selected from the group of:
    • (a) a polynucleotide sequence encoding a polypeptide, selected from the group consisting of SEQ ID NO: …(long list)
    • (b) a polynucleotide sequence encoding a polypeptide, selected from the group consisting of SEQ ID NO: … (long list)
    • (c) a polynucleotide sequence encoding the polypeptide sequence of (a) with conservative substitutions as defined in Table 2, wherein said polypeptide sequence of (a) with conservative substitutions is a transcription factor;
    • (d) a variant of the polynucleotide sequences of (a) or (b), which is at least 80% identical to a sequence of (a) or (b), and wherein said sequence variant encodes a polypeptide that is a transcription factor;
    • (e) an orthologous sequence of the polynucleotide sequences of (a) or (b), which is at least 80% identical to a sequence of (a) or (b), and wherein said orthologous sequence encodes a polypeptide;
    • (f) a paralogous sequence of the polynucleotide sequences of (a) or (b), which is at least 80% identical to a sequence of (a) or (b), and wherein said paralogous sequence encodes a polypeptide;
    • (g) a polynucleotide sequence encoding a polypeptide comprising a conserved domain that exhibits at least 80% sequence homology with the conserved domain of the polypeptide of (a), wherein said polypeptide comprising a conserved domain of a transcription factor; and wherein said conserved domain of (a) is bounded by amino acid residue coordinates according to Table 5; and
    • (h) a polynucleotide that hybridizes to the polynucleotide of (a) or (b) under stringent conditions.

A transgenic plant comprising the SEQ IDs listed above, including polynucleotides as in (a), transcription factors with conservative substitutions from (a), transcription factors at least 80% identical to (a) or (b), orthologous or paralogs at least 80% identical to (a) or (b), polynucleotides containing conserved domains at least 80% identical to conserved domains in (a) or (b), and polynucleotides that hybridise to those in (a) or (b) under stringent conditions.

  • An expression cassette comprising:
    • (1) a constitutive, inducible, or tissue-specific promoter; and
    • (2) a recombinant polynucleotide having a polynucleotide sequence, or a complementary polynucleotide sequence thereof, selected from the group consisting of:
      • (a) a polynucleotide sequence encoding a polypeptide, selected from the group of SEQ ID NO: …(long list)
      • (b) a polynucleotide sequence encoding a polypeptide, selected from the group of SEQ ID NO: …(long list)
      • (c) a polynucleotide sequence encoding the polypeptide sequence of (a) with conservative substitutions as defined in Table 2, wherein said polypeptide sequence of (a) with conservative substitutions is a transcription factor;
      • (d) a variant of the polynucleotide sequences of (a) or (b), which is at least 80% identical to a sequence of (a) or (b), and wherein said sequence variant encodes a polypeptide that is a transcription factor;
      • (e) an orthologous sequence of the polynucleotide sequences of (a) or (b), which is at least 80% identical to a sequence of (a) or (b), and wherein said orthologous sequence encodes a polypeptide that is a transcription factor;
      • (f) a paralogous sequence of the polynucleotide sequences of (a) or (b), which is at least 80% identical to a sequence of (a) or (b), and wherein said paralogous sequence encodes a polypeptide that is a transcription factor;
      • (g) a polynucleotide sequence encoding a polypeptide comprising a conserved domain that exhibits at least 80% sequence homology with the conserved domain of the polypeptide of (a), wherein said polypeptide comprising a conserved domain of a transcription factor; and wherein said conserved domain of (a) is bounded by amino acid residue coordinates according to Table 5; and
      • (h) a polynucleotide that hybridizes to the polynucleotide of (a) or (b) under stringent conditions; wherein said recombinant polynucleotide is operably linked to said promoter.

An expression cassette comprising, a promoter of (1) above, and containing a polynucleotide [as described above for claim 1]

  • A method for producing a modified plant having a modified trait, the method comprising:
    • (a) selecting a polynucleotide that encodes a polypeptide, wherein said polynucleotide has a sequence, or a complementary sequence thereof, selected from the group consisting of:
      • (i) a polynucleotide sequence encoding a polypeptide, selected from the group of SEQ ID NO: … (long list)
      • (ii) a polynucleotide sequence encoding a polypeptide, selected from the group of SEQ ID NO: … (longlist)
      • (iii) a polynucleotide sequence encoding the polypeptide sequence of (i) with conservative substitutions as defined in Table 2, wherein said polypeptide sequence of (i) with conservative substitutions is a transcription factor;
      • (iv) a variant of the polynucleotide sequences of (a) or (b), which is at least 80% identical to a sequence of (i) or (ii), and wherein said sequence variant encodes a polypeptide that is a transcription factor;
      • (v) an orthologous sequence of the polynucleotide sequences of (i) or (ii), which is at least 80% identical to a sequence of (i) or (ii), and wherein said orthologous sequence encodes a polypeptide that is a transcription factor;
      • (vi) a paralogous sequence of the polynucleotide sequences of (i) or (ii), which is at least 80% identical to a sequence of (i) or (ii), and wherein said paralogous sequence encodes a polypeptide that is a transcription factor;
      • (vii) a polynucleotide sequence encoding a polypeptide comprising a conserved domain that exhibits at least 80% sequence homology with the conserved domain of the polypeptide of (i), wherein said polypeptide comprising a conserved domain of a transcription factor; and wherein said conserved domain of (i) is bounded by amino acid residue coordinates according to Table 5, and
      • (viii) a polynucleotide that hybridizes to the polynucleotide of (i) or (ii) under stringent conditions; (b) inserting the polynucleotide into an expression cassette according to claim 92; (c) introducing the expression cassette into a plant or a cell of a plant to overexpress the polypeptide, thereby producing said modified plant; and (d) selecting said modified plant having said modified trait.

This time the claim is towards a method for producing a modified plant comprising a polynucleotide [as described above for claim 1]

The claims above are defined with reference to the sequences defined by SEQ ID numbers.  One interesting question here is the degree to which an examiner is able to effectively search for prior art.  It is not unreasonable to expect that the details of one or more transcription factors having at least 80% identical sequence to one or more of the SEQ IDs above may already be published in the literature or in another patent document.

Original Applicant:

Mendel Biotechnology, Inc. , 21375 Cabot Blvd., Hayward, CA, 94545,

For information concerning this application, we would suggest contacting either:

MATTHEW KASER Mendel Biotechnology, Inc. ,
21375 Cabot Blvd., , Hayward, CA, 94545,
(correspondent named on the application)

or:

Dr. William Goure,
Vice President for Commercial Development
Mendel Biotechnology, Inc.
21375 Cabot Boulevard
Hayward, CA 94545
t- 510 259 6122
wgoure@mendelbio.com

Remarks Again, as with the Paradigm patent applications mentioned above, it is unlikely that this application would result in a single granted patent for all of these sequence claims.  However, through numerous additional applications (continuations, CIPs and divisionals) it is entirely possible that any of the sequences listed may evolve into separate applications and may eventually be granted as patents.  Such a process may take many years.

Other interesting Mendel Biotechnology Inc. patent documents include

Document

Title

DNA Sequences
Claimed
US2003/0093837A1 Polynucleotides for seed trait alteration 74
US2004/0101481A1 Plant gene sequences I 85
US2003/0131386A1 Stress-induced polynucleotides 111
US2003/0229915A1 Plant gene sequences II 104
US2003/0233670A1 Gene sequences and uses thereof in plants 368
WO01/35725A1 Yield-related genes
35
WO02/15675A1 Genes for modifying plant traits IV
232