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Patent applications filed by the Scripps Research Institute, Syngenta Participations AG, and Koninklijke Philips Electronics N.V.

Technology overview

The patent family described in this section filed by the Scripps Research Institute, Syngenta Participations AG, and Koninklijke Philips Electronics N.V. discloses a DNA microarray-based detection method of plants that have been exposed to abiotic stress.  The technology describes a group of nucleotide sequences that have altered expression patterns when rice is exposed to abiotic stress conditions, in particular cold, saline and osmotic stress.  The description identifies use of the regulatory elements of these stress-responsive genes along with reporter genes (chloramphenicol acetyltransferase, CAT; ß-glucuronidase, GUS; green fluorescent protein, GFP; ß-galactosidase, ß-GAL; luciferase) as a means to produce transgenic plants that can act as biosentinels that detect the presence of abiotic stress conditions.  The related journal publication of this technology is Cooper et al. (2003).  A network of rice genes associated with stress response and seed development.  Proc Natl Acad Sci USA. 100(8):4945-4950.

Details of patent documents

Patent or Publication no.

Title, Independent Claims and Summary

Assignee and licensing information
CA 2420555

  • Earliest priority – 24 Aug 2000
  • Filed – 24 Aug 2001
  • Application pending
  • Expected expiry – not applicable
 Title – Stress-regulated genes of plants, transgenic plants containing same, and methods of use

Claim 1

A method of identifying a stress condition to which a plant cell has been exposed, the method comprising:
a) contacting nucleic acid molecules representative of expressed polynucleotides in the plant cell with an array of probes representative of the plant cell genome; and
b) detecting a profile of expressed polynucleotides in the plant cell characteristic of a stress response, thereby identifying the stress condition to which the plant cell was exposed.
Claim 18

A method for determining whether a test plant has been exposed to an abiotic stress, the method comprising

  • contacting nucleic acid molecules representative of expressed polynucleotides in cells of the test plant with at least one nucleic acid probe under conditions suitable for selective hybridization to a complementary nucleotide sequence, wherein

the probe comprises at least 15 nucleotides of a plant stress-regulated gene, provided said gene does not comprise a nucleotide sequence of a polynucleotide as set forth in any of SEQ ID NOS:156, 229, 233, 558, 573, 606, 635, 787, 813, 1263, 1386, 1391, 1405, 1445, 1484, 1589, 1609, 1634, 1726, 1866, 1918 or 1928, or a nucleotide sequence complementary thereto, whereby

detecting selective hybridization of at least one nucleic acid probe, or detecting a change in a level of selective hybridization as compared to a level of selective hybridization obtained using nucleic acid molecules representative of expressed polynucleotides in cells of a plant known not have been exposed to an abiotic stress, indicates that the test plant has been exposed to an abiotic stress, and whereby

an absence of selective hybridization of at least one nucleic acid probe indicates that the test plant has not been exposed to an abiotic stress.
Claim 22

A method for determining whether a test plant has been exposed to a cold stress, the method comprising

  • contacting nucleic acid molecules representative of expressed polynucleotides in cells of the test plant with at least one nucleic acid probe under conditions suitable for selective hybridization to a complementary nucleotide sequence, wherein

the probe comprises at least 15 nucleotides of a nucleotide sequence as set forth in any of SEQ ID NOS:1-155, 157-228, 230-232, 234-557, 559-572, 574-605, 607-634, 636-786, 788-812, 814-1261, or a nucleotide sequence complementary thereto, whereby

detecting selective hybridization of at least one nucleic acid probe, or detecting a change in a level of selective hybridization as compared to a level of selective hybridization obtained using nucleic acid molecules representative of expressed polynucleotides in cells of a plant known not have been exposed to a cold stress, indicates that the test plant has been exposed to a cold stress, and whereby

an absence of selective hybridization of at least one nucleic acid probe indicates that the test plant has not been exposed to a cold stress.
Claim 23

A method for determining whether a test plant has been exposed to a saline stress, the method comprising

  • contacting nucleic acid molecules representative of expressed polynucleotides in cells of the test plant with at least one nucleic acid probe under conditions suitable for selective hybridization to a complementary nucleotide sequence, wherein

the probe comprises at least 15 nucleotides of a nucleotide sequence as set forth in any of SEQ ID NOS:2226-2427, or a nucleotide sequence complementary thereto, whereby

detecting selective hybridization of at least one nucleic acid probe, or detecting a change in a level of selective hybridization as compared to a level of selective hybridization obtained using nucleic acid molecules representative of expressed polynucleotides in cells of a plant known not have been exposed to a saline stress, indicates that the test plant has been exposed to a saline stress, and whereby

an absence of selective hybridization of at least one nucleic acid probe indicates that the test plant has not been exposed to a saline stress.
Claim 24

A method for determining whether a test plant has been exposed to an osmotic stress, the method comprising

  • contacting nucleic acid molecules representative of expressed polynucleotides in cells of the test plant with at least one nucleic acid probe under conditions suitable for selective hybridization to a complementary nucleotide sequence, wherein

the probe comprises at least 15 nucleotides of a nucleotide sequence as set forth in two or more of SEQ ID NOS:2428-2585, or a nucleotide sequence complementary thereto, whereby

detecting selective hybridization of at least one nucleic acid probe, or detecting a change in a level of selective hybridization as compared to a level of selective hybridization obtained using nucleic acid molecules representative of expressed polynucleotides in cells of a plant known not have been exposed to an osmotic stress, indicates that the test plant has been exposed to an osmotic stress, and whereby

an absence of selective hybridization of at least one nucleic acid probe indicates that the test plant has not been exposed to an osmotic stress.
Claim 25

A method for determining whether a test plant has been exposed to a combination of abiotic stress conditions, the method comprising

  • contacting nucleic acid molecules representative of expressed polynucleotides in cells of the test plant with at least one nucleic acid probe under conditions suitable for selective hybridization to a complementary nucleotide sequence, whereby

detecting selective hybridization of at least one nucleic acid probe, or detecting a change in a level of selective hybridization as compared to a level of selective hybridization obtained using nucleic acid molecules representative of expressed polynucleotides in cells of a plant known not have been exposed to a combination of stress conditions, indicates that the test plant has been exposed to a combination of abiotic stress conditions, and whereby

an absence of selective hybridization of at least one nucleic acid probe indicates that the test plant has not been exposed to a combination of abiotic stress conditions.
Claim 30

A method for determining whether a test plant has been exposed to a cold stress and an osmotic stress, the method comprising

  • contacting nucleic acid molecules representative of expressed polynucleotides in cells of the test plant with at least one nucleic acid probe under conditions suitable for selective hybridization to a complementary nucleotide sequence, wherein

the probe comprises at least 15 nucleotides of a nucleotide sequence as set forth in any of SEQ ID NOS:1699-1969, or a nucleotide sequence complementary thereto, whereby

detecting selective hybridization of at least one nucleic acid probe, or detecting a change in a level of selective hybridization as compared to a level of selective hybridization obtained using nucleic acid molecules representative of expressed polynucleotides in cells of a plant known not have been exposed to a cold stress and an osmotic stress, indicates that the test plant has been exposed to a cold stress and an osmotic stress, and whereby

an absence of selective hybridization of at least one nucleic acid probe indicates that the test plant has not been exposed to a cold stress and an osmotic stress.
Claim 31

A method for determining whether a test plant has been exposed to a cold stress and a saline stress, the method comprising

  • contacting nucleic acid molecules representative of expressed polynucleotides in cells of the test plant with at least one nucleic acid probe under conditions suitable for selective hybridization to a complementary nucleotide sequence, wherein

the probe comprises at least 15 nucleotides of a nucleotide sequence as set forth in any of SEQ ID NOS:1970-2226, or a nucleotide sequence complementary thereto, whereby

detecting selective hybridization of at least one nucleic acid probe, or detecting a change in a level of selective hybridization as compared to a level of selective hybridization obtained using nucleic acid molecules representative of expressed polynucleotides in cells of a plant known not have been exposed to a cold stress and a saline stress, indicates that the test plant has been exposed to a cold stress and a saline stress, and whereby

an absence of selective hybridization of at least one nucleic acid probe indicates that the test plant has not been exposed to a cold stress and a saline stress.
Claim 32

A method for determining whether a test plant has been exposed to an osmotic stress and a saline stress, the method comprising

  • contacting nucleic acid molecules representative of expressed polynucleotides in the test plant with at least one nucleic acid probe under conditions suitable for selective hybridization to a complementary nucleotide sequence, wherein

the probe comprises at least 15 nucleotides of a nucleotide sequence as set forth in any of SEQ ID NOS:2586-2703, or a nucleotide sequence complementary thereto, whereby

detecting selective hybridization of at least one nucleic acid probe, or detecting a change in a level of selective hybridization as compared to a level of selective hybridization obtained using nucleic acid molecules representative of expressed polynucleotides in cells of a plant known not have been exposed to an osmotic stress and a saline stress, indicates that the test plant has been exposed to an osmotic stress and a saline stress, and whereby

an absence of selective hybridization of at least one nucleic acid probe indicates that the test plant has not been exposed to an osmotic stress and a saline stress.
Claim 33

A method for determining whether a test plant has been exposed to a cold stress, a saline stress and an osmotic stress, the method comprising

  • contacting nucleic acid molecules representative of expressed polynucleotides in cells of the test plant with a plurality of nucleic acid probes under conditions suitable for selective hybridization to a complementary nucleotide sequence, wherein

the probe comprises at least 15 nucleotides of a nucleotide sequence as set forth in any of SEQ ID NOS:1262-1698, or a nucleotide sequence complementary thereto, whereby

detecting selective hybridization of at least one nucleic acid probe, or detecting a change in a level of selective hybridization as compared to a level of selective hybridization obtained using nucleic acid molecules representative of expressed polynucleotides in cells of a plant known not have been exposed to a cold stress, a saline stress, and an osmotic stress, indicates that the test plant has been exposed to a cold stress, a saline stress and an osmotic stress, and whereby

an absence of selective hybridization of at least one nucleic acid probe indicates that the test plant has not been exposed to a cold stress, a saline stress and an osmotic stress.
Claim 34

A method for determining whether a test plant has been exposed to a cold stress, the method comprising

  • detecting a level of expression of at least one polynucleotide comprising a nucleotide sequence as set forth in SEQ ID NOS:1-155, 157-229, 230-232, 234-557, 559-572, 574-605, 607-634, 636-634, 636-786, 788812, and 814-1261 in cells of the test plant, wherein

detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to a cold stress, or detecting a level of expression that is less than about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to a cold stress, indicates the test plant has been exposed to a cold stress, or wherein

detecting a level of expression that is less than at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to a cold stress, or detecting a level of expression that is at least two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to a cold stress, indicates the test plant has not been exposed to a cold stress.
Claim 35

A method for determining whether a test plant has been exposed to a saline stress, the method comprising

  • detecting a level of expression of at least one polynucleotide comprising a nucleotide sequence as set forth in SEQ ID NOS:2226-2427 in cells of the test plant, wherein

detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to a saline stress, or detecting a level of expression that is less than about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to a saline stress, indicates the test plant has been exposed to a saline stress, or wherein

detecting a level of expression that is less than about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to a saline stress, or detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to a saline stress, indicates the test plant has not been exposed to a saline stress.
Claim 36

A method for determining whether a test plant has been exposed to an osmotic stress, the method comprising

  • detecting a level of expression of at least one polynucleotide comprising a nucleotide sequence as set forth in SEQ ID NOS:2428-2585 in cells of the test plant, wherein

detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to an osmotic stress, or detecting a level of expression that is less than about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to an osmotic stress, indicates the test plant has been exposed to a osmotic stress, or wherein

detecting a level of expression that is less than about two-fold different from level of expression of the at least one polynucleotide in cells of a plant not exposed to an osmotic stress, or detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to an osmotic stress, indicates the test plant has not been exposed to a osmotic stress.
Claim 37

A method for determining whether a test plant has been exposed to a cold stress and an osmotic stress, the method comprising

  • detecting a level of expression of at least one polynucleotide comprising a nucleotide sequence as set forth in SEQ ID NOS:1699-1969 in cells of the test plant, wherein

detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to a cold stress and an osmotic stress, or detecting a level of expression that is less than about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to a cold stress and an osmotic stress, indicates the test plant has been exposed to a cold stress and an osmotic stress, or wherein

detecting a level of expression that is less than about two-fold different from as a level of expression of the at least one polynucleotide in cells of a plant not exposed to a cold stress and an osmotic stress, or detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to a cold stress and an osmotic stress, indicates the test plant has not been exposed to a cold stress and an osmotic stress.
Claim 38

A method for determining whether a test plant has been exposed to a cold stress and a saline stress, the method comprising

  • detecting a level of expression of at least one polynucleotide comprising a nucleotide sequence as set forth in SEQ ID NOS:1970-2226 in cells of the test plant, wherein

detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to a cold stress and a saline stress, or detecting a level of expression that is less than about two-fold different from as a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to a cold stress and a saline stress, indicates the test plant has been exposed to a cold stress and a saline stress, or wherein

detecting a level of expression that is less than about two-fold different from as a level of expression of the at least one polynucleotide in cells of a plant not exposed to a cold stress and a saline stress, or detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to a cold stress and a saline stress, indicates the test plant has not been exposed to a cold stress and a saline stress.
Claim 39

A method for determining whether a test plant has been exposed to a saline stress and an osmotic stress, the method comprising

  • detecting a level of expression of at least one polynucleotide comprising a nucleotide sequence as set forth in SEQ ID NOS:2586-2703 in cells of the test plant, wherein

detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to a saline stress and an osmotic stress, or detecting a level of expression that is less than about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to a saline stress and an osmotic stress, indicates the test plant has been exposed to a saline stress and an osmotic stress, or wherein

detecting a level of expression that is less than about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to a saline stress and an osmotic stress, or detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to saline stress and an osmotic stress, indicates the test plant has not been exposed to a saline stress and an osmotic stress.
Claim 40

A method for determining whether a test plant has been exposed to a cold stress, the method comprising

  • detecting a level of expression of at least one polynucleotide comprising a nucleotide sequence as set forth SEQ ID NOS:1-155, 157-229, 230-232, 234-557, 559-572, 574-605, 607-634, 636-634, 636-786, 788812, and 814-1261 in cells of the test plant, wherein

detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to a cold stress, or detecting a level of expression that is less than about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to a cold stress, indicates the test plant has been exposed to a cold stress, or wherein

detecting a level of expression that is less than about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to a cold stress, or detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to a cold stress, indicates the test plant has not been exposed to a cold stress.
Claim 41

A method for determining whether a test plant has been exposed to a cold stress, a saline stress and an osmotic stress, the method comprising

  • detecting a level of expression of at least one polynucleotide comprising a nucleotide sequence as set forth in SEQ ID NOS:1262-1698 in cells of the test plant, wherein

detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to a cold stress, a saline stress and an osmotic stress, or detecting a level of expression that is less than about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to a cold stress, a saline stress and an osmotic stress, indicates the test plant has been exposed to a cold stress, a saline stress and an osmotic stress, or wherein

detecting a level of expression that is less than about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to a cold stress, a saline stress and an osmotic stress, or detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to a cold stress, a saline stress and an osmotic stress, indicates the test plant has not been exposed to a cold stress, a saline stress and an osmotic stress.
Claim 42

A method of producing a transgenic plant comprising plant cells that exhibit altered responsiveness to at least one stress condition, the method comprising

  • introducing a polynucleotide portion of a plant stress-regulated gene into a plant cell genome, wherein the polynucleotide portion of the stress-regulated gene does not comprise a nucleotide sequence as set forth in any of SEQ ID NOS:156, 229, 233, 558, 573, 606, 635, 787, 813, 1263, 1386, 1391, 1405, 1445, 1484, 1589, 1609, 1634, 1726, 1866, 1918 or 1928, whereby the polynucleotide portion of the plant stress-regulated gene modulates a response of the plant cells to at least one stress condition, thereby producing a transgenic plant comprising plant cells that exhibit altered responsiveness to the stress condition.
Claim 46

A method of producing a transgenic plant comprising plant cells that exhibit altered responsiveness to a combination of at least two stress conditions, the method comprising

  • introducing a polynucleotide portion of a plant stress-regulated gene into a plant cell genome, whereby the polynucleotide portion of the plant stress-regulated gene modulates a response of the plant cells to a combination of at least two stress conditions, thereby producing a transgenic plant comprising plant cells that exhibit altered responsiveness to the stress conditions.
Claim 85

A method of selecting a plant having an altered resistance to an abiotic stress condition or a combination of abiotic stress conditions, the method comprising:

a) contacting nucleic acid molecules representative of expressed polynucleotides in a plant cell of a plant to be examined for having an altered resistance to an abiotic stress with a nucleic acid probes that selectively hybridizes under stringent conditions to a plant stress-regulated gene comprising a nucleotide sequence as set forth in any of SEQ ID NO:1-5379;

b) detecting a level of selective hybridization of the nucleic acid probes to a nucleic acid molecule representative of an expressed polynucleotide in the plant cell, wherein the level of selective hybridization corresponds to the level of the expressed polynucleotide in the plant cell, which is indicative of resistance of the plant to an abiotic stress; and

c) selecting a plant having a level of expression of a polynucleotide indicative of altered resistance to an abiotic stress condition.
Claim 96A method of modulating the responsiveness of a plant cell to a stress condition, the method comprising

  • introducing a polynucleotide portion of a plant stress-regulated gene into the plant cell, wherein said gene comprises a nucleotide sequence of a polynucleotide as set forth in any of SEQ ID NOS:1-155, 157-228, 230-232, 234-557, 559-572, 574-605, 607-634, 636-786, 788-812, 814-1262, 1264-1386, 1387-1390, 1392-1404, 1406-1444, 1446-1483, 1485-1588, 1590-1608, 1610-1633, 1634-1725, 1727-1865, 1867-1917, 1919-1927, 1929-2855, 2857-2928, 2930-2932, 2934-3256, 3258-3271, 3273-3304, 3306-3323, 3325-3333, 3335-3485, 3487-3511, 3313-3956, 3958-4078, 4080-4097, 4099-4136, 4138-4175, 4177-4279, 4281-4299, 4301-4324, 4326-4414, 4416-4552, 4554-4602, and 4604-5379, thereby modulating the responsiveness of the plant cell to a stress condition.
Claim 115A method of expressing a heterologous nucleotide sequence in a plant cell, the method comprising

  • introducing into the plant cell a plant stress-regulated regulatory element operatively linked to the heterologous nucleotide sequence, wherein said regulatory element comprises a nucleotide sequence as set forth in any of SEQ ID NOS:2704-2855, 2857-2928, 2930-2932, 2934-3256, 3258-3271, 3273-3304, 3306-3323, 3325-3333, 3335-3485, 3487-3511, 3313-3956, 3958-4078, 4080-4097, 4099-4136, 4138-4175, 4177-4279, 4281-4299, 4301-4324, 4326-4414, 4416-4552, 4554-4602, and 4604-5379, whereby, upon exposure of the plant cell to stress condition, the heterologous nucleotide sequence is expressed in the plant cell.
Claim 119A method of modulating the activity of a biological pathway in a plant cell involving a plant stress-regulated polypeptide, the method comprising

  • introducing a polynucleotide portion of a plant stress-regulated gene into the plant cell, wherein the plant stress-regulated gene comprises a nucleotide sequence as set forth in any of SEQ ID NOS:1-155, 157-228, 230-232, 234-557, 559-572, 574-605, 607-634, 636-786, 788-812, 814-1262, 1264-1386, 1387-1390, 1392-1404, 1406-1444, 1446-1483, 1485-1588, 1590-1608, 1610-1633, 1634-1725, 1727-1865,1867-1917, 1919-1927, 1929-2855, 2857-2928, 2930-2932, 2934-3256, 3258-3271, 3273-3304, 3306-3323, 3325-3333, 3335-3485, 3487-3511, 3313-3956, 3958-4078, 4080-4097, 4099-4136, 4138-4175, 4177-4279, 4281-4299, 4301-4324, 4326-4414, 4416-4552, 4554-4602, and 4604-5379, thereby modulating the activity of the biological pathway.
Claim 122A method of identifying a polynucleotide that modulates a stress response in a plant cell, the methods comprising:

a) contacting an array of probes representative of a plant cell genome and nucleic acid molecules expressed in plant cell exposed to the stress;

b) detecting a nucleic acid molecule that is expressed at a level different from a level of expression in the absence of the stress;

c) introducing the nucleic acid molecule of step b) into a plant cell; and

d) detecting a modulated response of the plant cell of step c) to a stress, thereby identifying a polynucleotide that modulates a stress response in a plant cell.
Claim 127A transgenic plant, which contains a transgene comprising a polynucleotide portion of plant stress-regulated gene, wherein the gene comprises

  • a nucleotide sequence as set forth in any of SEQ ID NOS:1-155, 157-228, 230-232, 234-SS7, 559-572, 574-605, 607-634, 636-786, 788-812, 814-1262, 1264-1386, 1387-1390, 1392-1404, 1406-1444, 1446-1483, 1485-1588, 1590-1608, 1610-1633, 1634-1725, 1727-1865, 1867-1917, 1919-1927, 1929-2855, 2857-2928, 2930-2932, 2934-3256, 3258-3271, 3273-3304, 3306-3323, 3325-3333, 3335-3485, 3487-3511, 3313-3956, 3958-4078, 4080-4097, 4099-4136, 4138-4175, 4177-4279, 4281-4299, 4301-4324, 4326-4414, 4416-4552, 4554-4602, and 4604-5379.
Claim 142A plant stress-regulated gene regulatory element, wherein the gene comprises

  • a nucleotide sequence as set forth in any of SEQ ID NOS:1-155, 157228, 230-232, 234-557, 559-572, 574-605, 607-634, 636-786, 788-812, 814-1262, 1264-1386, 1387-1390, 1392-1404, 1406-1444, 1446-1483, 1485-1588, 1590-1608, 1610-1633, 1634-1725, 1727-1865, 1867-1917, 1919-1927, 1929-2855, 2857-2928, 2930-2932, 2934-3256, 3258-3271, 3273-3304, 3306-3323, 3325-3333, 3335-3485, 3487-3511, 3313-3956, 3958-4078, 4080-4097, 4099-4136, 4138-4175, 4177-4279, 4281-4299, 4301-4324, 4326-4414, 4416-4552, 4554-4602, and 4604-5379.
Claim 154A method for identifying a polynucleotide involved in a stress response of a plant, the method comprising:

a) contacting nucleic acid molecules representative of expressed polynucleotides in plant cells of a plant exposed to a stress condition or combination of stress conditions with an array of probes representative of the plant cell genome; and

b) detecting a nucleic acid molecule that exhibits at least a two-fold change in the level of expression as compared to the level of the nucleic acid molecule in a corresponding plant cell of a plant that was not exposed to the stress condition, thereby identifying a polynucleotide involved in a stress response of the plant.
Claim 157A computer readable medium having stored thereon computer executable instructions for performing a method comprising:

a) receiving data on expression in a cell of a plant of a nucleic acid molecule having at least 70% sequence identity to a nucleotide sequence comprising any of SEQ ID NO. 1-5379; and

b) comparing the data on expression of the nucleic acid molecule with data on expression of the nucleic acid in a cell of a plant that has not been exposed to an abiotic stress, of a plant that has been exposed to an abiotic stress condition or combination of abiotic stress conditions, or of a combination of such plants.
Claim 159A computer-readable medium having stored thereon a data structure comprising:

  • sequence data for at least one nucleic acid molecule having at least 70% nucleic acid sequence identity to a polynucleotide having a nucleotide sequence as set forth in any of SEQ ID NO. 1-5379 or a nucleotide sequence complementary thereto; and
  • a module receiving the nucleic acid molecule sequence data, which compares the nucleic acid molecule sequence data to a least one other nucleic acid sequence.

The claims are generally drawn towards:

  • a method of identifying a stress condition to which a plant cell has been exposed (claim 1)
  • a method for determining whether a test plant has been exposed to an abiotic stress (claim 18; 22, 34 and 40: cold stress; 23 and 35: saline stress; 24 and 36: osmotic stress)
  • a method for determining whether a test plant has been exposed to a combination of abiotic stress conditions (claim 25; 30 and 37: cold and osmotic stress; 31 and 38: cold and saline stress; 32 and 39: osmotic and saline stress; 33 and 41: cold, saline and osmotic stress)
  • a method of producing a transgenic plant that exhibit altered responsiveness to at least one stress condition (claim 42)
  • a method of producing a transgenic plant that exhibit altered responsiveness to at least two stress conditions (claim 46)
  • a method for monitoring a population of plants for exposure to a stress condition or a combination of stress conditions (claim 68)
  • a method of selecting a plant having an altered resistance to an abiotic stress condition or a combination of abiotic stress conditions (claim 85)
  • a method of modulating the responsiveness of a plant cell to a stress condition (claim 96)
  • a method of expressing a heterologous nucleotide sequence in a plant cell (claim 115)
  • a method of modulating the activity of a biological pathway in a plant cell involving a plant stress-regulated polypeptide (claim 119)
  • a method of identifying a polynucleotide that modulates a stress response in a plant cell (claim 122)
  • a transgenic plant containing a transgene comprising a polynucleotide portion of plant stress-regulated gene (claim 127)
  • a plant stress-regulated gene regulatory element (claim 142)
  • a method for identifying a polynucleotide involved in a stress response of a plant (claim 154)
  • a computor readable medium having stored executable instructions for comparing data on expression in a cell of a plant (claim 157)
  • a computor readable medium having stored a data structure comprising sequence data and a module (claim 159)

Definitions extracted from the specification are:

  • Abiotic stress – exposure of a plant, plant cell, or the like, to a non-living (“abiotic”) physical or chemical agent or condition that has an adverse effect on metabolism, growth, development, propagation and/or survival of the plant (collectively “growth”).
  • SEQ ID NOS:156, 229, 233, 558, 573, 606, 635, 787, 813, 1263, 1386, 1391, 1405, 1445, 1484, 1589, 1609, 1634, 1726, 1866, 1918 or 1928 – (polynucleotides that) previously have been described as being involved in a stress-regulated response in plants… and, therefore, are not encompassed, in whole or in part, within the compositions of the invention…
  • SEQ ID NOS:1-155, 157-228, 230-232, 234-557, 559-572, 574-605, 607-634, 636-786, 788-812, 814-1261 (SEQ ID NOS 1-1261 excluding ones previously described, see dot point above) – cold responsive genes
  • SEQ ID NOS:2226 – 2427 – saline responsive genes
  • SEQ ID NOS:2428 – 2585 – osmotic responsive genes
  • SEQ ID NOS:1699 – 1969 – cold and osmotic responsive genes
  • SEQ ID NOS:1970 – 2226 – cold and saline responsive genes
  • SEQ ID NOS:2586 – 2703 – osmotic and saline responsive genes
  • SEQ ID NOS:1262 – 1698 – cold, osmotic and saline responsive genes
  • SEQ ID NOS:1 – 5379 – this list is categorised into two groups: SEQ ID NOS:1 – 2703 – stress-regulated polypeptide or functional peptide portion thereof; SEQ ID NOS:2704 – 5379 – stress-regulated gene regulatory element
  • SEQ ID NOS:2704-2855, 2857-2928, 2930-2932, 2934-3256, 3258-3271, 3273-3304, 3306-3323, 3325-3333, 3335-3485, 3487-3511, 3313-3956, 3958-4078, 4080-4097, 4099-4136, 4138-4175, 4177-4279, 4281-4299, 4301-4324, 4326-4414, 4416-4552, 4554-4602, and 4604-5379 – stress-regulated gene regulatory elements excluding those for which the corresponding stress responsive genes have been previously described.
  • Plant stress-regulated gene – a polynucleotide sequence of a plant, the transcription of which is altered in response to exposure to a stress condition, and the regulatory elements linked to such a polynulceotide sequence and involved in the stress response, which can be induction or repression.
  • Regulatory element – a nucleotide sequence that, when operatively linked to a coding region of a genes, affects transcription of the coding region such that a ribonucleic acid (RNA) molecule is transcribed from the coding region.
  • Plant stress-regulated regulatory element – a nucleotide sequence of a plant genome that can respond to a stress such that expression of a gene product encoded by a gene comprising the regulatory element (a stress-inducible gene) is increased above or decreased below the level of expression of the gene product in the absence of the stress condition.
  • Operatively linked (in reference to a regulatory element) – the regulatory element is positioned with respect to a second nucleotide sequence such that the regulatory element affects transcription or transcription and translation of the nucleotide sequence in substantially the same manner, but not necessarily to the same extent, as is does when the regulatory element is present in its natural position in a genome.
  • Heterologous nucleotide sequence – a nucleotide sequence that is not normally part of the plant stress-regulated gene from which the polynucleotide portion of the plant stress-regulated gene-component of the recombinant polynucleotide is obtained; or, if it is a part of the plant stress-regulated gene from which the polynucleotide portion is obtained, it is an orientation other than it would normall be in…
  • Introducing (a polynucleotide portion) – transferring a polynucleotide into a plant cell. The method is not limited to Agrobacterium-mediated transformation.
  • At least one (nucleic acid probe) – includes one, two, three or more…
  • Pluarity (of nucleic acid probes) – two or more…

Comments:

Since this is a published application and not a granted patent, currently there are no enforceable rights.

Dependent claims 144-149 are generally drawn towards a method to identify agents by use of transgenic bioreporter systems (which corresponds to dependent claims 146-151 in WO 2002/16655, see below for content).

 Scripps Research Institute

10550 NORTH TORREY PINES ROAD
LA JOLLA, CALIFORNIA 92037

Syngenta Participations AG

SCHWARZWALDALLEE 215
CH-4058 BASEL, SWITZERLAND

Koninklijke Philips Electronics N.V.

(US only)

GROENEWOUDSEWEG 1
EINDHOVEN, NETHERLANDS 5621
US 2002/160378

US 2004/009476(corrected publication)

  • Earliest priority – 24 Aug 2000
  • Filed – 24 Aug 2001
  • Application pending
  • Expected expiry – not applicable
 Title – Stress-regulated genes of plants, transgenic plants containing same, and methods of use

Claim 1
A method for determining whether a test plant has been exposed to an abiotic stress condition, the method comprising

  • contacting nucleic acid molecules representative of expressed polynucleotides in cells of the test plant with at least one nucleic acid probe under conditions suitable for selective hybridization to a complementary nucleotide sequence, wherein

the probe comprises at least 15 nucleotides of a nucleotide sequence as set forth in any of SEQ ID NOS:1-155, 157-228, 230-232, 234-557, 559-572, 574-605, 607-634, 636-786, 788-812, 814-1261, 2227-2585, 2704-2857-2928, 2930-2932, 2934-3256, 3258-3271, 3273-3304, 3306-3323, 3325-3333, 3335-3485, 3487-3511, 3313-3955, and 4910-5263, or a nucleotide sequence complementary thereto, whereby

detecting selective hybridization of at least one nucleic acid probe, or detecting a change in a level of selective hybridization as compared to a level of selective hybridization obtained using nucleic acid molecules representative of expressed polynucleotides in cells of a plant known not have been exposed to an abiotic stress, indicates that the test plant has been exposed to an abiotic stress condition, and whereby

an absence of selective hybridization of at least one nucleic acid probe indicates that the test plant has not been exposed to an abiotic stress condition.
Claim 5
A method for determining whether a test plant has been exposed to a combination of abiotic stress conditions, the method comprising

  • contacting nucleic acid molecules representative of expressed polynucleotides in cells of the test plant with at least one nucleic acid probe under conditions suitable for selective hybridization to a complementary nucleotide sequence, wherein

the probe comprises at least 15 nucleotides of a nucleotide sequence as set forth in any of SEQ ID NOS:1262-2226, 2586-2703, 3956-4909, and 5264-5379, or a nucleotide sequence complementary thereto, whereby

detecting selective hybridization of at least one nucleic acid probe, or detecting a change in a level of selective hybridization as compared to a level of selective hybridization obtained using nucleic acid molecules representative of expressed polynucleotides in cells of a plant known not have been exposed to a combination of stress conditions, indicates that the test plant has been exposed to a combination of abiotic stress conditions, and whereby

an absence of selective hybridization of at least one nucleic acid probe indicates that the test plant has not been exposed to a combination of abiotic stress conditions.
Claim 12
A method for determining whether a test plant has been exposed to an abiotic stress condition or combination of abiotic stress conditions, the method comprisingdetecting a level of expression of at least one polynucleotide comprising a nucleotide sequence as set forth in any of SEQ ID NOS:1-155, 157-228, 230-232, 234-557, 559-572, 574-605, 607-634, 636-786, 788-812, 814-1262, 1264-1386, 1387-1390, 1392-1404, 1406-1444, 1446-1483, 1485-1588, 1590-1608, 1610-1633, 1634-1725, 1727-1865, 1867-1917, 1919-1927, 1929-2855, 2857-2928, 2930-2932, 2934-3256, 3258-3271, 3273-3304, 3306-3323, 3325-3333, 3335-3485, 3487-3511, 3313-3956, 3958-4078, 4080-4097, 4099-4136, 4138-4175, 4177-4279, 4281-4299, 4301-4324, 4326-4414, 4416-4552, 4554-4602, and 4604-5379, in cells of the test plant, wherein

detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to an abiotic stress or combination of abiotic stresses, or detecting a level of expression that is less than about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to an abiotic stress or combination of abiotic stresses, indicates the test plant has been exposed to an abiotic stress or combination of abiotic stresses, or wherein

detecting a level of expression that is less than at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to an abiotic stress or combination of abiotic stresses, or detecting a level of expression that is at least two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to an abiotic stress or combination of abiotic stresses, indicates the test plant has not been exposed to an abiotic stress or combination of abiotic stresses.
Claim 20
A method of identifying a stress condition to which a plant cell has been exposed, the method comprising:a) contacting nucleic acid molecules representative of expressed polynucleotides in the plant cell with an array of probes representative of the plant cell genome; and

b) detecting a profile of expressed polynucleotides in the plant cell characteristic of a stress response, thereby identifying the stress condition to which the plant cell was exposed.
Claim 29
A method of producing a transgenic plant comprising plant cells that exhibit altered responsiveness to at least one stress condition, the method comprising

  • introducing a polynucleotide portion of a plant stress-regulated gene into a plant cell genome, wherein

the polynucleotide portion of the stress-regulated gene comprises a nucleotide sequence as set forth in any of 1-155, 157-228, 230-232, 234-557, 559-572, 574-605, 607-634, 636-786, 788-812, 814-1262, 1264-1386, 1387-1390, 1392-1404, 1406-1444, 1446-1483, 1485-1588, 1590-1608, 1610-1633, 1634-1725, 1727-1865, 1867-1917, 1919-1927, 1929-2855, 2857-2928, 2930-2932, 2934-3256, 3258-3271, 3273-3304, 3306-3323, 3325-3333, 3335-3485, 3487-3511, 3313-3956, 3958-4078, 4080-4097, 4099-4136, 4138-4175, 4177-4279, 4281-4299, 4301-4324, 4326-4414, 4416-4552, 4554-4602, and 4604-5379, whereby the polynucleotide portion of the plant stress-regulated gene modulates a response of the plant cells to at least one stress condition, thereby producing a transgenic plant comprising plant cells that exhibit altered responsiveness to the stress condition.
Claim 46
A transgenic plant, which contains a transgene comprising a polynucleotide portion of plant stress-regulated gene, wherein the gene comprises

  • a nucleotide sequence as set forth in any of SEQ ID NOS:1-155, 157-228, 230-232, 234-557, 559-572, 574-605, 607-634, 636-786, 788-812, 814-1262, 1264-1386, 1387-1390, 1392-1404, 1406-1444, 1446-1483, 1485-1588, 1590-1608, 1610-1633, 1634-1725, 1727-1865, 1867-1917, 1919-1927, 1929-2855, 2857-2928, 2930-2932, 2934-3256, 3258-3271, 3273-3304, 3306-3323, 3325-3333, 3335-3485, 3487-3511, 3313-3956, 3958-4078, 4080-4097, 4099-4136, 4138-4175, 4177-4279, 4281-4299, 4301-4324, 4326-4414, 4416-4552, 4554-4602, and 4604-5379.
Claim 58
A plant stress-regulated gene regulatory element, wherein the gene comprises

  • a nucleotide sequence as set forth in any of SEQ ID NOS:1-155, 157-228, 230-232, 234-557, 559-572, 574-605, 607-634, 636-786, 788-812, 814-1262, 1264-1386, 1387-1390, 1392-1404, 1406-1444, 1446-1483, 1485-1588, 1590-1608, 1610-1633, 1634-1725, 1727-1865, 1867-1917, 1919-1927, 1929-2855, 2857-2928, 2930-2932, 2934-3256, 3258-3271, 3273-3304, 3306-3323, 3325-3333, 3335-3485, 3487-3511, 3313-3956, 3958-4078, 4080-4097, 4099-4136, 4138-4175, 4177-4279, 4281-4299, 4301-4324, 4326-4414, 4416-4552, 4554-4602, and 4604-5379.
Claim 66
A method of selecting a plant having an altered resistance to an abiotic stress condition or a combination of abiotic stress conditions, the method comprising:a) contacting nucleic acid molecules representative of expressed polynucleotides in a plant cell of a plant to be examined for having an altered resistance to an abiotic stress with a nucleic acid probe that selectively hybridizes under stringent conditions to a plant stress-regulated gene comprising a nucleotide sequence as set forth in any of SEQ ID NO:1-155, 157-228, 230-232, 234-557, 559-572, 574-605, 607-634, 636-786, 788-812, 814-1262, 1264-1386, 1387-1390, 1392-1404, 1406-1444, 1446-1483, 1485-1588, 1590-1608, 1610-1633, 1634-1725, 1727-1865, 1867-1917, 1919-1927, 1929-2855, 2857-2928, 2930-2932, 2934-3256, 3258-3271, 3273-3304, 3306-3323, 3325-3333, 3335-3485, 3487-3511, 3313-3956, 3958-4078, 4080-4097, 4099-4136, 4138-4175, 4177-4279, 4281-4299, 4301-4324, 4326-4414, 4416-4552, 4554-4602, and 4604-5379;

b) detecting a level of selective hybridization of the nucleic acid probes to a nucleic acid molecule representative of an expressed polynucleotide in the plant cell, wherein the level of selective hybridization corresponds to the level of the expressed polynucleotide in the plant cell, which is indicative of resistance of the plant to an abiotic stress; and

c) selecting a plant having a level of expression of a polynucleotide indicative of altered resistance to an abiotic stress condition.
Claim 75
A method for identifying a polynucleotide involved in a stress response of a plant, the method comprising:a) contacting nucleic acid molecules representative of expressed polynucleotides in plant cells of a plant exposed to a stress condition or combination of stress conditions with an array of probes representative of the plant cell genome; and

b) detecting a nucleic acid molecule that exhibits at least a two-fold change in the level of expression as compared to the level of the nucleic acid molecule in a corresponding plant cell of a plant that was not exposed to the stress condition, thereby identifying a polynucleotide involved in a stress response of the plant.
Claim 78
A computer readable medium having stored thereon computer executable instructions for performing a method comprising:a) receiving data on expression in a cell of a plant of a nucleic acid molecule having at least 70% sequence identity to a nucleotide sequence comprising any of SEQ ID NO. 1-5379; and

b) comparing the data on expression of the nucleic acid molecule with data on expression of the nucleic acid in a cell of a plant that has not been exposed to an abiotic stress, of a plant that has been exposed to an abiotic stress condition or combination of abiotic stress conditions, or of a combination of such plants.
Claim 79
A computer-readable medium having stored thereon a data structure comprising:

  • sequence data for at least one nucleic acid molecule having at least 70% nucleic acid sequence identity to a polynucleotide having a nucleotide sequence as set forth in any of SEQ ID NO. 1-5379 or a nucleotide sequence complementary thereto; and
  • a module receiving the nucleic acid molecule sequence data, which compares the nucleic acid molecule sequence data to a least one other nucleic acid sequence.

The claims are generally drawn towards:

  • a method for determining whether a test plant has been exposed to an abiotic stress condition (claim 1)
  • a method for determining whether a test plant has been exposed to a combination of abiotic stress conditions (claim 5)
  • a method for determining whether a test plant has been exposed to an abiotic stress condition or combination of abiotic stress conditions (claim 12)
  • a method of identifying a stress condition to which a plant cell has been exposed (claim 20)
  • a method of producing a transgenic plant comprising plant cells that exhibit altered responsiveness to at least one stress condition (claim 29)
  • a transgenic plant, which contains a transgene comprising a polynucleotide portion of plant stress-regulated gene (claim 46)
  • a plant stress-regulated gene regulatory element (claim 58)
  • a method of selecting a plant having an altered resistance to an abiotic stress condition or a combination of abiotic stress conditions (claim 66)
  • a method for identifying a polynucleotide involved in a stress response of a plant (claim 75)
  • A computer-readable medium having stored thereon a data structure comprising sequence data and a module (claim 79)

Definitions extracted from the specification are provided in CA 2420555.

Comments:

Since this is a published application and not a granted patent, currently there are no enforceable rights.

Dependent claims 71-74 are generally drawn towards a method to identify agents by use of stress-responsive regulatory elements linked to nucleotide sequences coding for reporter molecules (which corresponds to dependent claims 146-149 in WO2002/16655, see below for content).
WO 2002/16655 A2

WO 2002/16655 A2 R6
(corrected publication)

  • Earliest priority – 24 Aug 2000
  • Filed – 24 Aug 2001
  • Published – 28 Feb 2002
  • Corrected – 9 Jan 2003
  • Expected expiry – not applicable
 Title – Stress-regulated genes of plants, transgenic plants containing same, and methods of use

Claim 1

A method of identifying a stress condition to which a plant cell has been exposed, the method comprising:
a) contacting nucleic acid molecules representative of expressed polynucleotides in the plant cell with an array of probes representative of the plant cell genome; and
b) detecting a profile of expressed polynucleotides in the plant cell characteristic of a stress response, thereby identifying the stress condition to which the plant cell was exposed.
Claim 18

A method for determining whether a test plant has been exposed to an abiotic stress, the method comprising

  • contacting nucleic acid molecules representative of expressed polynucleotides in cells of the test plant with at least one nucleic acid probe under conditions suitable for selective hybridization to a complementary nucleotide sequence, wherein

the probe comprises at least 15 nucleotides of a plant stress-regulated gene, provided said gene does not comprise a nucleotide sequence of a polynucleotide as set forth in any of SEQ ID NOS:156, 229, 233, 558, 573, 606, 635, 787, 813, 1263, 1386, 1391, 1405, 1445, 1484, 1589, 1609, 1634, 1726, 1866, 1918 or 1928,or a nucleotide sequence complementary thereto, whereby

detecting selective hybridization of at least one nucleic acid probe, or detecting a change in a level of selective hybridization as compared to a level of selective hybridization obtained using nucleic acid molecules representative of expressed polynucleotides in cells of a plant known not have been exposed to an abiotic stress, indicates that the test plant has been exposed to an abiotic stress, and whereby

an absence of selective hybridization of at least one nucleic acid probe indicates that the test plant has not been exposed to an abiotic stress.
Claim 22

A method for determining whether a test plant has been exposed to a cold stress, the method comprising

  • contacting nucleic acid molecules representative of expressed polynucleotides in cells of the test plant with at least one nucleic acid probe under conditions suitable for selective hybridization to a complementary nucleotide sequence, wherein

the probe comprises at least 15 nucleotides of a nucleotide sequence as set forth in any of SEQ ID NOS:1-155, 157-228, 230-232, 234-557, 559-572, 574-605, 607-634, 636-786, 788-812, 814-1261, or a nucleotide sequence complementary thereto, whereby

detecting selective hybridization of at least one nucleic acid probe, or detecting a change in a level of selective hybridization as compared to a level of selective hybridization obtained using nucleic acid molecules representative of expressed polynucleotides in cells of a plant known not have been exposed to a cold stress, indicates that the test plant has been exposed to a cold stress, and whereby

an absence of selective hybridization of at least one nucleic acid probe indicates that the test plant has not been exposed to a cold stress.
Claim 23

A method for determining whether a test plant has been exposed to a saline stress, the method comprising

  • contacting nucleic acid molecules representative of expressed polynucleotides in cells of the test plant with at least one nucleic acid probe under conditions suitable for selective hybridization to a complementary nucleotide sequence, wherein

the probe comprises at least 15 nucleotides of a nucleotide sequence as set forth in any of SEQ ID NOS:2226-2427, or a nucleotide sequence complementary thereto, whereby

detecting selective hybridization of at least one nucleic acid probe, or detecting a change in a level of selective hybridization as compared to a level of selective hybridization obtained using nucleic acid molecules representative of expressed polynucleotides in cells of a plant known not have been exposed to a saline stress, indicates that the test plant has been exposed to a saline stress, and whereby

an absence of selective hybridization of at least one nucleic acid probe indicates that the test plant has not been exposed to a saline stress.
Claim 24

A method for determining whether a test plant has been exposed to an osmotic stress, the method comprising

  • contacting nucleic acid molecules representative of expressed polynucleotides in cells of the test plant with at least one nucleic acid probe under conditions suitable for selective hybridization to a complementary nucleotide sequence, wherein

the probe comprises at least 15 nucleotides of a nucleotide sequence as set forth in two or more of SEQ ID NOS:2428-2585, or a nucleotide sequence complementary thereto, whereby

detecting selective hybridization of at least one nucleic acid probe, or detecting a change in a level of selective hybridization as compared to a level of selective hybridization obtained using nucleic acid molecules representative of expressed polynucleotides in cells of a plant known not have been exposed to an osmotic stress, indicates that the test plant has been exposed to an osmotic stress, and whereby

an absence of selective hybridization of at least one nucleic acid probe indicates that the test plant has not been exposed to an osmotic stress.
Claim 25

A method for determining whether a test plant has been exposed to a combination of abiotic stress conditions, the method comprising

  • contacting nucleic acid molecules representative of expressed polynucleotides in cells of the test plant with at least one nucleic acid probe under conditions suitable for selective hybridization to a complementary nucleotide sequence, whereby

detecting selective hybridization of at least one nucleic acid probe, or detecting a change in a level of selective hybridization as compared to a level of selective hybridization obtained using nucleic acid molecules representative of expressed polynucleotides in cells of a plant known not have been exposed to a combination of stress conditions, indicates that the test plant has been exposed to a combination of abiotic stress conditions, and whereby

an absence of selective hybridization of at least one nucleic acid probe indicates that the test plant has not been exposed to a combination of abiotic stress conditions.
Claim 30

A method for determining whether a test plant has been exposed to a cold stress and an osmotic stress, the method comprising

  • contacting nucleic acid molecules representative of expressed polynucleotides in cells of the test plant with at least one nucleic acid probe under conditions suitable for selective hybridization to a complementary nucleotide sequence, wherein

the probe comprises at least 15 nucleotides of a nucleotide sequence as set forth in any of SEQ ID NOS:1699-1969, or a nucleotide sequence complementary thereto, whereby

detecting selective hybridization of at least one nucleic acid probe, or detecting a change in a level of selective hybridization as compared to a level of selective hybridization obtained using nucleic acid molecules representative of expressed polynucleotides in cells of a plant known not have been exposed to a cold stress and an osmotic stress, indicates that the test plant has been exposed to a cold stress and an osmotic stress, and whereby

an absence of selective hybridization of at least one nucleic acid probe indicates that the test plant has not been exposed to a cold stress and an osmotic stress.
Claim 31

A method for determining whether a test plant has been exposed to a cold stress and a saline stress, the method comprising

  • contacting nucleic acid molecules representative of expressed polynucleotides in cells of the test plant with at least one nucleic acid probe under conditions suitable for selective hybridization to a complementary nucleotide sequence, wherein

the probe comprises at least 15 nucleotides of a nucleotide sequence as set forth in any of SEQ ID NOS:1970-2226, or a nucleotide sequence complementary thereto, whereby

detecting selective hybridization of at least one nucleic acid probe, or detecting a change in a level of selective hybridization as compared to a level of selective hybridization obtained using nucleic acid molecules representative of expressed polynucleotides in cells of a plant known not have been exposed to a cold stress and a saline stress, indicates that the test plant has been exposed to a cold stress and a saline stress, and whereby

an absence of selective hybridization of at least one nucleic acid probe indicates that the test plant has not been exposed to a cold stress and a saline stress.
Claim 32

A method for determining whether a test plant has been exposed to an osmotic stress and a saline stress, the method comprising

  • contacting nucleic acid molecules representative of expressed polynucleotides in the test plant with at least one nucleic acid probe under conditions suitable for selective hybridization to a complementary nucleotide sequence, wherein

the probe comprises at least 15 nucleotides of a nucleotide sequence as set forth in any of SEQ ID NOS:2586-2703, or a nucleotide sequence complementary thereto, whereby

detecting selective hybridization of at least one nucleic acid probe, or detecting a change in a level of selective hybridization as compared to a level of selective hybridization obtained using nucleic acid molecules representative of expressed polynucleotides in cells of a plant known not have been exposed to an osmotic stress and a saline stress, indicates that the test plant has been exposed to an osmotic stress and a saline stress, and whereby

an absence of selective hybridization of at least one nucleic acid probe indicates that the test plant has not been exposed to an osmotic stress and a saline stress.
Claim 33

A method for determining whether a test plant has been exposed to a cold stress, a saline stress and an osmotic stress, the method comprising

  • contacting nucleic acid molecules representative of expressed polynucleotides in cells of the test plant with a plurality of nucleic acid probes under conditions suitable for selective hybridization to a complementary nucleotide sequence, wherein

the probe comprises at least 15 nucleotides of a nucleotide sequence as set forth in any of SEQ ID NOS:1262-1698, or a nucleotide sequence complementary thereto, whereby

detecting selective hybridization of at least one nucleic acid probe, or detecting a change in a level of selective hybridization as compared to a level of selective hybridization obtained using nucleic acid molecules representative of expressed polynucleotides in cells of a plant known not have been exposed to a cold stress, a saline stress, and an osmotic stress, indicates that the test plant has been exposed to a cold stress, a saline stress and an osmotic stress, and whereby

an absence of selective hybridization of at least one nucleic acid probe indicates that the test plant has not been exposed to a cold stress, a saline stress and an osmotic stress.
Claim 34

A method for determining whether a test plant has been exposed to a cold stress, the method comprising

  • detecting a level of expression of at least one polynucleotide comprising a nucleotide sequence as set forth in SEQ ID NOS:1-155, 157-229, 230-232, 234-557, 559-572, 574-605, 607-634, 636-634, 636-786, 788812, and 814-1261 in cells of the test plant, wherein

detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to a cold stress, or detecting a level of expression that is less than about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to a cold stress, indicates the test plant has been exposed to a cold stress, or wherein

detecting a level of expression that is less than at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to a cold stress, or detecting a level of expression that is at least two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to a cold stress, indicates the test plant has not been exposed to a cold stress.
Claim 35

A method for determining whether a test plant has been exposed to a saline stress, the method comprising

  • detecting a level of expression of at least one polynucleotide comprising a nucleotide sequence as set forth in SEQ ID NOS:2226-2427 in cells of the test plant, wherein

detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to a saline stress, or detecting a level of expression that is less than about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to a saline stress, indicates the test plant has been exposed to a saline stress, or wherein

detecting a level of expression that is less than about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to a saline stress, or detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to a saline stress, indicates the test plant has not been exposed to a saline stress.
Claim 36

A method for determining whether a test plant has been exposed to an osmotic stress, the method comprising

  • detecting a level of expression of at least one polynucleotide comprising a nucleotide sequence as set forth in SEQ ID NOS:2428-2585 in cells of the test plant, wherein

detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to an osmotic stress, or detecting a level of expression that is less than about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to an osmotic stress, indicates the test plant has been exposed to a osmotic stress, or wherein

detecting a level of expression that is less than about two-fold different from level of expression of the at least one polynucleotide in cells of a plant not exposed to an osmotic stress, or detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to an osmotic stress, indicates the test plant has not been exposed to a osmotic stress.
Claim 37

A method for determining whether a test plant has been exposed to a cold stress and an osmotic stress, the method comprising

  • detecting a level of expression of at least one polynucleotide comprising a nucleotide sequence as set forth in SEQ ID NOS:1699-1969 in cells of the test plant, wherein

detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to a cold stress and an osmotic stress, or detecting a level of expression that is less than about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to a cold stress and an osmotic stress, indicates the test plant has been exposed to a cold stress and an osmotic stress, or wherein

detecting a level of expression that is less than about two-fold different from as a level of expression of the at least one polynucleotide in cells of a plant not exposed to a cold stress and an osmotic stress, or detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to a cold stress and an osmotic stress, indicates the test plant has not been exposed to a cold stress and an osmotic stress.
Claim 38

A method for determining whether a test plant has been exposed to a cold stress and a saline stress, the method comprising

  • detecting a level of expression of at least one polynucleotide comprising a nucleotide sequence as set forth in SEQ ID NOS:1970-2226 in cells of the test plant, wherein

detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to a cold stress and a saline stress, or detecting a level of expression that is less than about two-fold different from as a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to a cold stress and a saline stress, indicates the test plant has been exposed to a cold stress and a saline stress, or wherein

detecting a level of expression that is less than about two-fold different from as a level of expression of the at least one polynucleotide in cells of a plant not exposed to a cold stress and a saline stress, or detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to a cold stress and a saline stress, indicates the test plant has not been exposed to a cold stress and a saline stress.
Claim 39

A method for determining whether a test plant has been exposed to a saline stress and an osmotic stress, the method comprising

  • detecting a level of expression of at least one polynucleotide comprising a nucleotide sequence as set forth in SEQ ID NOS:2586-2703 in cells of the test plant, wherein

detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to a saline stress and an osmotic stress, or detecting a level of expression that is less than about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to a saline stress and an osmotic stress, indicates the test plant has been exposed to a saline stress and an osmotic stress, or wherein

detecting a level of expression that is less than about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to a saline stress and an osmotic stress, or detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to saline stress and an osmotic stress, indicates the test plant has not been exposed to a saline stress and an osmotic stress.
Claim 40

A method for determining whether a test plant has been exposed to a cold stress, the method comprising

  • detecting a level of expression of at least one polynucleotide comprising a nucleotide sequence as set forth SEQ ID NOS:1-155, 157-229, 230-232, 234-557, 559-572, 574-605, 607-634, 636-634, 636-786, 788812, and 814-1261 in cells of the test plant, wherein

detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to a cold stress, or detecting a level of expression that is less than about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to a cold stress, indicates the test plant has been exposed to a cold stress, or wherein

detecting a level of expression that is less than about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to a cold stress, or detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to a cold stress, indicates the test plant has not been exposed to a cold stress.
Claim 41

A method for determining whether a test plant has been exposed to a cold stress, a saline stress and an osmotic stress, the method comprising

  • detecting a level of expression of at least one polynucleotide comprising a nucleotide sequence as set forth in SEQ ID NOS:1262-1698 in cells of the test plant, wherein

detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to a cold stress, a saline stress and an osmotic stress, or detecting a level of expression that is less than about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to a cold stress, a saline stress and an osmotic stress, indicates the test plant has been exposed to a cold stress, a saline stress and an osmotic stress, or wherein

detecting a level of expression that is less than about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant not exposed to a cold stress, a saline stress and an osmotic stress, or detecting a level of expression that is at least about two-fold different from a level of expression of the at least one polynucleotide in cells of a plant known to be exposed to a cold stress, a saline stress and an osmotic stress, indicates the test plant has not been exposed to a cold stress, a saline stress and an osmotic stress.
Claim 42

A method of producing a transgenic plant comprising plant cells that exhibit altered responsiveness to at least one stress condition, the method comprising

  • introducing a polynucleotide portion of a plant stress-regulated gene into a plant cell genome, wherein the polynucleotide portion of the stress-regulated gene does not comprise a nucleotide sequence as set forth in any of SEQ ID NOS:156, 229, 233, 558, 573, 606, 635, 787, 813, 1263, 1386, 1391, 1405, 1445, 1484, 1589, 1609, 1634, 1726, 1866, 1918 or 1928, whereby the polynucleotide portion of the plant stress-regulated gene modulates a response of the plant cells to at least one stress condition, thereby producing a transgenic plant comprising plant cells that exhibit altered responsiveness to the stress condition.
Claim 46

A method of producing a transgenic plant comprising plant cells that exhibit altered responsiveness to a combination of at least two stress conditions, the method comprising

  • introducing a polynucleotide portion of a plant stress-regulated gene into a plant cell genome, whereby the polynucleotide portion of the plant stress-regulated gene modulates a response of the plant cells to a combination of at least two stress conditions, thereby producing a transgenic plant comprising plant cells that exhibit altered responsiveness to the stress conditions.
Claim 85

A method of selecting a plant having an altered resistance to an abiotic stress condition or a combination of abiotic stress conditions, the method comprising:

a) contacting nucleic acid molecules representative of expressed polynucleotides in a plant cell of a plant to be examined for having an altered resistance to an abiotic stress with a nucleic acid probes that selectively hybridizes under stringent conditions to a plant stress-regulated gene comprising a nucleotide sequence as set forth in any of SEQ ID NO:1-5379;

b) detecting a level of selective hybridization of the nucleic acid probes to a nucleic acid molecule representative of an expressed polynucleotide in the plant cell, wherein the level of selective hybridization corresponds to the level of the expressed polynucleotide in the plant cell, which is indicative of resistance of the plant to an abiotic stress; and

c) selecting a plant having a level of expression of a polynucleotide indicative of altered resistance to an abiotic stress condition.
Claim 96A method of modulating the responsiveness of a plant cell to a stress condition, the method comprising

  • introducing a polynucleotide portion of a plant stress-regulated gene into the plant cell, wherein said gene comprises a nucleotide sequence of a polynucleotide as set forth in any of SEQ ID NOS:1-155, 157-228, 230-232, 234-557, 559-572, 574-605, 607-634, 636-786, 788-812, 814-1262, 1264-1386, 1387-1390, 1392-1404, 1406-1444, 1446-1483, 1485-1588, 1590-1608, 1610-1633, 1634-1725, 1727-1865, 1867-1917, 1919-1927, 1929-2855, 2857-2928, 2930-2932, 2934-3256, 3258-3271, 3273-3304, 3306-3323, 3325-3333, 3335-3485, 3487-3511, 3313-3956, 3958-4078, 4080-4097, 4099-4136, 4138-4175, 4177-4279, 4281-4299, 4301-4324, 4326-4414, 4416-4552, 4554-4602, and 4604-5379, thereby modulating the responsiveness of the plant cell to a stress condition.
Claim 117A method of expressing a heterologous nucleotide sequence in a plant cell, the method comprising

  • introducing into the plant cell a plant stress-regulated regulatory element operatively linked to the heterologous nucleotide sequence, wherein said regulatory element comprises a nucleotide sequence as set forth in any of SEQ ID NOS:2704-2855, 2857-2928, 2930-2932, 2934-3256, 3258-3271, 3273-3304, 3306-3323, 3325-3333, 3335-3485, 3487-3511, 3313-3956, 3958-4078, 4080-4097, 4099-4136, 4138-4175, 4177-4279, 4281-4299, 4301-4324, 4326-4414, 4416-4552, 4554-4602, and 4604-5379, whereby, upon exposure of the plant cell to stress condition, the heterologous nucleotide sequence is expressed in the plant cell.
Claim 121A method of modulating the activity of a biological pathway in a plant cell involving a plant stress-regulated polypeptide, the method comprising

  • introducing a polynucleotide portion of a plant stress-regulated gene into the plant cell, wherein the plant stress-regulated gene comprises a nucleotide sequence as set forth in any of SEQ ID NOS:1-155, 157-228, 230-232, 234-557, 559-572, 574-605, 607-634, 636-786, 788-812, 814-1262, 1264-1386, 1387-1390, 1392-1404, 1406-1444, 1446-1483, 1485-1588, 1590-1608, 1610-1633, 1634-1725, 1727-1865,1867-1917, 1919-1927, 1929-2855, 2857-2928, 2930-2932, 2934-3256, 3258-3271, 3273-3304, 3306-3323, 3325-3333, 3335-3485, 3487-3511, 3313-3956, 3958-4078, 4080-4097, 4099-4136, 4138-4175, 4177-4279, 4281-4299, 4301-4324, 4326-4414, 4416-4552, 4554-4602, and 4604-5379, thereby modulating the activity of the biological pathway.
Claim 124A method of identifying a polynucleotide that modulates a stress response in a plant cell, the methods comprising:

a) contacting an array of probes representative of a plant cell genome and nucleic acid molecules expressed in plant cell exposed to the stress;

b) detecting a nucleic acid molecule that is expressed at a level different from a level of expression in the absence of the stress;

c) introducing the nucleic acid molecule of step b) into a plant cell; and

d) detecting a modulated response of the plant cell of step c) to a stress, thereby identifying a polynucleotide that modulates a stress response in a plant cell.
Claim 129A transgenic plant, which contains a transgene comprising a polynucleotide portion of plant stress-regulated gene, wherein the gene comprises

  • a nucleotide sequence as set forth in any of SEQ ID NOS:1-155, 157-228, 230-232, 234-SS7, 559-572, 574-605, 607-634, 636-786, 788-812, 814-1262, 1264-1386, 1387-1390, 1392-1404, 1406-1444, 1446-1483, 1485-1588, 1590-1608, 1610-1633, 1634-1725, 1727-1865, 1867-1917, 1919-1927, 1929-2855, 2857-2928, 2930-2932, 2934-3256, 3258-3271, 3273-3304, 3306-3323, 3325-3333, 3335-3485, 3487-3511, 3313-3956, 3958-4078, 4080-4097, 4099-4136, 4138-4175, 4177-4279, 4281-4299, 4301-4324, 4326-4414, 4416-4552, 4554-4602, and 4604-5379.
Claim 144A plant stress-regulated gene regulatory element, wherein the gene comprises

  • a nucleotide sequence as set forth in any of SEQ ID NOS:1-155, 157228, 230-232, 234-557, 559-572, 574-605, 607-634, 636-786, 788-812, 814-1262, 1264-1386, 1387-1390, 1392-1404, 1406-1444, 1446-1483, 1485-1588, 1590-1608, 1610-1633, 1634-1725, 1727-1865, 1867-1917, 1919-1927, 1929-2855, 2857-2928, 2930-2932, 2934-3256, 3258-3271, 3273-3304, 3306-3323, 3325-3333, 3335-3485, 3487-3511, 3313-3956, 3958-4078, 4080-4097, 4099-4136, 4138-4175, 4177-4279, 4281-4299, 4301-4324, 4326-4414, 4416-4552, 4554-4602, and 4604-5379.
Claim 156A method for identifying a polynucleotide involved in a stress response of a plant, the method comprising:

a) contacting nucleic acid molecules representative of expressed polynucleotides in plant cells of a plant exposed to a stress condition or combination of stress conditions with an array of probes representative of the plant cell genome; and

b) detecting a nucleic acid molecule that exhibits at least a two-fold change in the level of expression as compared to the level of the nucleic acid molecule in a corresponding plant cell of a plant that was not exposed to the stress condition, thereby identifying a polynucleotide involved in a stress response of the plant.
Claim 159A computer readable medium having stored thereon computer executable instructions for performing a method comprising:

a) receiving data on expression in a cell of a plant of a nucleic acid molecule having at least 70% sequence identity to a nucleotide sequence comprising any of SEQ ID NO. 1-5379; and

b) comparing the data on expression of the nucleic acid molecule with data on expression of the nucleic acid in a cell of a plant that has not been exposed to an abiotic stress, of a plant that has been exposed to an abiotic stress condition or combination of abiotic stress conditions, or of a combination of such plants.
Claim 161A computer-readable medium having stored thereon a data structure comprising:

  • sequence data for at least one nucleic acid molecule having at least 70% nucleic acid sequence identity to a polynucleotide having a nucleotide sequence as set forth in any of SEQ ID NO. 1-5379 or a nucleotide sequence complementary thereto; and
  • a module receiving the nucleic acid molecule sequence data, which compares the nucleic acid molecule sequence data to a least one other nucleic acid sequence.

The claims are generally drawn towards:

  • a method of identifying a stress condition to which a plant cell has been exposed (claim 1)
  • a method for determining whether a test plant has been exposed to an abiotic stress (claim 18; 22, 34 and 40: cold stress; 23 and 35: saline stress; 24 and 36: osmotic stress)
  • a method for determining whether a test plant has been exposed to a combination of abiotic stress conditions (claim 25; 30 and 37: cold and osmotic stress; 31 and 38: cold and saline stress; 32 and 39: osmotic and saline stress; 33 and 41: cold, saline and osmotic stress)
  • a method of producing a transgenic plant that exhibit altered responsiveness to at least one stress condition (claim 42)
  • a method of producing a transgenic plant that exhibit altered responsiveness to at least two stress conditions (claim 46)
  • a method for monitoring a population of plants for exposure to a stress condition or a combination of stress conditions (claim 68)
  • a method of selecting a plant having an altered resistance to an abiotic stress condition or a combination of abiotic stress conditions (claim 85)
  • a method of modulating the responsiveness of a plant cell to a stress condition (claim 96)
  • a method of expressing a heterologous nucleotide sequence in a plant cell (claim 117)
  • a method of modulating the activity of a biological pathway in a plant cell involving a plant stress-regulated polypeptide (claim 121)
  • a method of identifying a polynucleotide that modulates a stress response in a plant cell (claim 124)
  • a transgenic plant containing a transgene comprising a polynucleotide portion of plant stress-regulated gene (claim 129)
  • a plant stress-regulated gene regulatory element (claim 144)
  • a method for identifying a polynucleotide involved in a stress response of a plant (claim 156)
  • a computor readable medium having stored executable instructions for comparing data on expression in a cell of a plant (claim 159)
  • a computor readable medium having stored a data structure comprising sequence data and a module (claim 161)

Definitions extracted from the specification are provided in CA 2420555.

Comments:

Since this is a published application and not a granted patent, there are no enforceable rights.

Dependent claims 146-151 are generally drawn towards a method to identify agents by use of bioreporter systems as follows:

  • a method to identify an agent that modulates the activity of the plant stress-regulated regulatory element (claim 146),
  • where the regulatory element may be linked to a heterologous nucleotide sequence (claim 147),
  • where the heterologous nucleotide sequence may encode for a reporter molecule (claim 148),
  • and the regulatory element/reporter system is in a plant (in vivo, in situ) or in vitro (claim 149),
  • where the plant (in claim 149) is a transgenic plant containing the regulatory element/reporter gene (claim 150),
  • that detects a stress mimicing agent (claim 151).
Remarks
  1. National phase entry of WO 2002/16655 in Australia (AU 2001/86811) is pending.
  2. National phase entry of WO 2002/16655 in Europe (EP 1313867) is deemed to be withdrawn on 26 Apr 2006.

Search strategy

Search details
Date of search 11/05/2006
Database searched Patent Lens
Type of search Expert, stemming off
Collections searched AU-B, US-A, US-B, EP-B, WO
Search terms (sentinel near/5 plant) or (sentinel near/5 organism)
Results 9
Comments Of the 9 results identified using these search terms, 6 results were identified as being of particular interest based on their abstracts and a review of their claims.