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Patent applications filed by Syngenta Participations AG

Technology overview

A research team lead by Dr Jeffrey F. Harper at the Torrey Mesa Research Institute, Syngenta, used GeneChip microarray to conduct global expression profiling of Arabidopsis thalianasubjected to cold, saline, and osmotic stress (journal publication related to this technology is Kreps et al. (2002).  Transcriptome changes for Arabidopsis in response to salt, osmotic, and cold stress.  Plant Physiol. 130(4):2129-41).  Identified genes and their regulatory elements, and methods of their use were subsequently claimed in the PCT application introduced in this section.  The national phase entry of WO 2003/008540 in the US (US 2006/075523) claims for stress-responsive polypeptides and corresponding polynucleotides, but not for the associated regulatory elements that may be used as promoters in a bioindicator system.  Therefore the US patent application may not be relevant to the scope of this technology landscape.

Details of patent documents

Patent or Publication no.

Title, Independent Claims and Summary

Assignee and licensing information
US 2006/075523

  • Earliest priority – 22 Jun 2001
  • Filed – 14 Sept 2005
  • Application pending
  • Expected expiry – not applicable
 Title – Abiotic stress responsive polynucleotides and polypeptides

NOTE: THIS APPLICATION DOES NOT CLAIM ANY REGULATORY ELEMENTS THAT MAY ACT AS STRESS-INDUCIBLE PROMOTERS NOR REPORTER ELEMENTS THAT MAY BE LINKED TO SUCH PROMOTER SEQUENCES. THEREFORE THIS PATENT APPLICATION IS OUT OF THE SCOPE OF THIS LANDSCAPE.

Claim 1
An isolated nucleic acid molecule comprising a polynucleotide selected from the group consisting of:a) any one of the nucleotide sequences selected from the group consisting of SEQ ID NOs. 1-4;

b) a functional portion of any of the sequences of a);

c) a polynucleotide that is substantially similar to a sequence of a) or b);

d) a sequence of at least 15 nucletides that hybridizes under stringent conditions to a polynucleotide of a), b) or c);

e) the complement of any sequence of a), b), c) or d);

f) the reverse complement of any sequence of a), b), c) or d);

g) a polynucleotide encoding any polypeptide selected from the group consisting of SEQ ID NOs. 5-8; and

h) an allelic variant of any of the above.
Claim 26
An isolated polypeptide comprising:a) any one of the amino acid sequences selected from the group consisting of SEQ ID NOs. 5-8;

b) a functional portion of a);

c) an amino acid sequence substantially similar to any sequence of a) or b);

d) an amino acid sequence of a)-c) wherein there has been at least one conservative amino acid substitution;

e) an allelic variant of any of a)-d).
Claim 27
A method for altering the tolerance of a plant to an abiotic stress comprising

  • introducing into said plant a recombinant nucleic acid construct comprising at least one of the polynucleotides selected from the group consisting of SEQ ID NOs. 1-4.
Claim 28
A method for altering the tolerance of a plant to an abiotic stress comprising

  • introducing into said plant a recombinant nucleic acid construct comprising a polynucleotide of at least 15 nucleotides in length that hybridizes under high stringency conditions to the complement of a sequence selected from the group consisting of SEQ ID NOs. 1-4.
Claim 30
A method for altering the tolerance of a plant to an abiotic stress comprising

  • introducing into said plant a recombinant nucleic acid construct, wherein

said construct encodes a molecule which alters expression of an abiotic stress regulated coding region selected from the group consisting of SEQ ID NOs. 1-4, or the complement thereof.
Claim 34
A method for selecting an agent that alters abiotic stress regulated polynucleotide expression in a plant cell comprising:

  • contacting at least one plant cell with a test agent;
  • subjecting said plant cell to an abiotic stress before, during or after contacting said plant cell with said test agent;
  • obtaining an expression profile of said plant cell wherein said expression profile comprises expression data for at least one abiotic stress regulated sequence selected from the group consisting of SEQ ID NOs. 1-4.;
  • comparing the expression profile of said cell to the expression profile obtained from at least one plant cell not exposed to said agent, but exposed to said abiotic stress;
  • selecting said agent if said agent alters expression of said abiotic stress regulated sequence.

The claims are generally drawn towards:

  • an isolated nucleic acid molecule comprising a polynucleotide (claim 1)
  • an isolated polypeptide (claim 26)
  • a method for altering the tolerance of a plant to an abiotic stress (claim 27, 28, 30)
  • a method for selecting an agent that alters abiotic stress regulated polynucleotide expression in a plant cell (claim 34)

Definitions extracted from the description are:

  • SEQ ID NOs. 1-4 – nucleotide sequence(s) containing a coding region for abiotic stress responsive polypeptide(s)
  • SEQ ID NOs. 5-8 – encoded polypeptide sequence(s) of SEQ ID NOs. 1-4
  • Functional portion – a contiguous nucleotide sequence of the plant stress-regulated sequence that provides a function within a plant or plant cell
  • Substantially similar (nucleotide sequence) – a nucleotide sequence corresponding to a reference nucleotide sequence, wherein the corresponding sequence encodes a polypeptide having substantially the same structure and function as the polypeptide encoded by the reference nucleotide sequence, e.g., where only changes in amino acids not affecting the polypeptide function occur

Comments:

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

SEQ ID information from NCBI:

Based on the nucleotide-nucleotide BLAST search the four polynucleotide SEQ IDs were identified as

  • SEQ ID NO:1 – RNA polymerase B transcription factor 3 (BFT3); NCBI accession no. AY224525
  • SEQ ID NO:2 – Unknown protein, amino acid search for SEQ ID NO:6 identified as containing the heavy metal associated domain (HMA); NCBI accession no. NP918616
  • SEQ ID NO:3 – Adenosine kinase-like protein; NCBI accession no. AY224510
  • SEQ ID NO:4 – Putative farnesyltransferase (FT; amino acid search for SEQ ID NO:8 identified as the beta subunit of FT); NCBI accession no. NM191123
 Syngenta Participations AG

SCHWARZWALDALLEE 215
CH-4058 BASEL, SWITZERLAND
WO 2003/008540

  • Earliest priority – 22 Jun 2001
  • Filed – 21 Jun 2002
  • Published – 30 Jan 2003
  • Expected expiry – not applicable
 Title – Abiotic stress responsive polynucleotides and polypeptides

Claim 1
An isolated nucleic acid molecule comprising a polynucleotide selected from the group consisting of:a) any one of the nucleotide sequences selected from the group consisting of SEQ ID NOs. 1-4131, 8263-8353, 8445-8829 and 17505-17506;
b) a functional portion of any of the sequences of a);
c) a polynucleotide that is substantially similar to a sequence of a) or b);
d) a sequence of at least 15 nucletides that hybridizes under stringent conditions to a polynucleotide of a), b) or c);
e) the complement of any sequence of a), b), c) or d);
f) the reverse complement of any sequence of a), b), c) or d);
g) a polynucleotide encoding any polypeptide selected from the group consisting of SEQ ID NOs. 4132-8262, 8354-8444, and 8830-9214; and
h) an allelic variant of any of the above.
Claim 26
An isolated polypeptide comprising:a) any one of the amino acid sequences selected from the group consisting of SEQ ID NOs. 4132-8262, 8354-8444, and 8830-9214;
b) a functional portion of a);
c) an amino acid sequence to any sequence of a) or b);
d) an amino acid sequence of a)-c) wherein there has been at least one conservative amino acid substitution;
e) an allelic variant of any of a)-d).
Claim 34
A method for determining whether a test plant has been exposed to at least one abiotic stress condition comprising,

  • determining expression of a plurality of polynucleotides selected from the group consisting of SEQ ID NOs. 1-4131, 8263-8353, 8445-8829 and 17505-17506 in said test plant to produce an expression profile, and
  • comparing said expression profile of said test plant to an expression profile for the same plurality of polynucleotides in a reference plant exposed to at least one abiotic stress.
Claim 48
A method for altering the tolerance of a plant to an abiotic stress comprising

  • introducing into said plant a recombinant nucleic acid construct comprising at least one of the polynucleotides selected from the group consisting of SEQ lD NOs. 1-4131, 8263-8353, 8445-8829, and 11374-17506.
CLaim 49
A method for altering the tolerance of a plant to an abiotic stress comprising

  • introducing into said plant a recombinant nucleic acid construct comprising a polynucleotide of at least 15 nucleotides in length that hybridizes under high stringency conditions to the complement of a sequence selected from the group consisting of SEQ ID NOs. 1-4131, 8263-8353, 8445-8829, and 17505-17506.
Claim 51
A method for altering the tolerance of a plant to an abiotic stress comprising

  • introducing into said plant a recombinant nucleic acid construct, wherein said construct encodes a molecule which alters expression of an abiotic stress regulated coding region selected from the group consisting of SEQ ID NOs. 1-4131, 8263-8353, 8445-8829, and 17505-17506, or the complement thereof.
Claim 55
A method for selecting an agent that alters abiotic stress regulated polynucleotide expression in a plant cell comprising:

  • contacting at least one plant cell with a test agent;
  • subjecting said plant cell to an abiotic stress before, during or after contacting said plant cell with said test agent;
  • obtaining an expression profile of said plant cell wherein said expression profile comprises expression data for at least one abiotic stress regulated sequence selected from the group consisting of SEQ ID NOs. 1-4131, 8263-8353, 8445-8829, and 17505-17506.;
  • comparing the expression profile of said cell to the expression profile obtained from at least one plant cell not exposed to said agent, but exposed to said abiotic stress;
  • selecting said agent if said agent alters expression of said abiotic stress regulated sequence.
Claim 61
A computer readable medium having stored thereon computer executable instructions for performing a method comprising,

  • receiving data on expression in a test plant of at least one polynucleotide having at least 70% sequence identity to a nucleotide sequence selected from the group consisting of SEQ ID NOs. 1-4131, 8263-8353, 8445-8829, and 17505-17506, or the complement thereof and
  • comparing expression data from said test plant to expressin data for the same at least one nucleic acid molecule in a plant which has been exposed to at least one abiotic stress.
Claim 62
A computer-readable medium having stored thereon a data structure comprising,

  • sequence data for at least one polynucleotide having at least 70% nucleic acid sequence identity to a polynucleotide selected from the group consisting of SEQ ID NOs. 1-4131, 8263-8353, 8445-8829, and 17505-17506, or the complement thereof; and
  • a module receiving the nucleic acid molecule sequence data which compares the nucleic acid molecule sequence data to at least one other nucleic acid sequence.
Claim 65
A method for identifying a homolog or ortholog to an abiotic stress responsive polynucleotide comprising:a) determining the nucleotide sequence of a plurality of isolated polynucleotides to create a set of nucleotide sequences;
b) translating the nucleotide sequences in the set to derive one or more putative amino acid sequences, based on one or more of the possible reading frames of the nucleotide sequences and their complementary sequences;
c) selecting an amino acid sequence of an abiotic stress-responsive protein and comparing the amino acid sequence of the abiotic stress-responsive protein with at least one of the putative amino acid sequences;
d) identifying putative amino acid sequences having homology with at least a region of the amino acid sequence of the abiotic stress-responsive protein; and
e) correlating putative amino acid sequences having said homology to translated nucleotide sequences of b).
Claim 68
A method for altering the expression of a polynucleotide in response to an abiotic stress comprising

  • operably linking said polynucleotide to a regulatory region selected from the group consisting of SEQ ID NOs. 13374-17504.

The claims are generally drawn towards:

  • an isolated nucleic acid molecule comprising a polynucleotide containing a coding region for an abiotic stress responsive polypeptide (claim 1)
  • an isolated polypeptide comprising a stress-regulated polypeptide (claim 26)
  • a method for determining whether a test plant has been exposed to at least one abiotic stress condition (claim 34)
  • a method for altering the tolerance of a plant to an abiotic stress (claim 48, 49, 51)
  • a method for selecting an agent that alters abiotic stress regulated polynucleotide expression in a plant cell (claim 55)
  • a computer readable medium having stored thereon computer executable instructions for receiving and comparing expression data (claim 61)
  • a computer-readable medium having stored thereon a data structure comprising sequence data and a module (claim 62)
  • a method for identifying a homolog or ortholog to an abiotic stress responsive polynucleotide (claim 65)
  • a method for altering the expression of a polynucleotide in response to an abiotic stress (claim 68)

Definitions extracted from the description are:

  • SEQ ID NOs. 1-4131, 8263-8353, 8445-8829 and 17505-17506 – nucleotide sequence(s) containing a coding region for an abiotic stress responsive polypeptide
  • SEQ ID NOs. 4132-8262, 8354-8444, and 8830-9214 – amino acid (polypeptide) sequences of abiotic stress responsive polypeptides
  • SEQ ID NOs. 13374-17504 – nucleotide sequences comprising regulatory elements of nucleotide sequence(s) coding for abiotic stress responsive polypeptides
  • Isolated nucleic acid – nucleic acid sequence that is free of one or both of the nucleotide sequences which flank the polynucleotide in the naturally-occurring genome of the organism from which the polynucleotide is derived
  • Abiotic stress condition – 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”)
  • Substantially similar (nucleotide sequence) – a nucleotide sequence corresponding to a reference nucleotide sequence, wherein the corresponding sequence encodes a polypeptide having substantially the same structure and function as the polypeptide encoded by the reference nucleotide sequence, e.g., where only changes in amino acids not affecting the polypeptide function occur. Specific hybridization conditions for this term is provided in the specification.
  • Substantially similar (polypeptide) – an amino acid sequence relative to a reference (query) sequence shares at least about 65% amino acid sequence identity, at least about 75% amino acid sequence identity, at least about 85%, at least about 90% , or at least about 95% or greater amino acid sequence identity
  • Regulatory region – a nucleotide sequence that, when operatively linked to a coding region, effects transcription of the coding region such that a ribonucleic acid (RNA) molecule is transcribed from the coding region
  • Operably link(ed) – the regulatory element is positioned with respect to a second nucleotide sequence such that the regulatory element effects transcription or transcription and translation of the nucleotide sequence in substantially the same manner, but not necessarily to the same extent, as it does when the regulatory element is present in its natural position in a genome
  • Coding region – include(s) a nucleotide sequence of a genomic DNA or a cDNA molecule comprising all or part of a coding region of the coding strand
  • Stringent conditions – hybridizes (to the reference nucleotide sequence) in 7% sodium dodecyl sulfate (SDS), 0.5 M NaPO4, I mM EDTA at 50˚C with washing in 2X SSC, 0.1% SDS at 50˚C; in 7% sodium dodecyl sulfate (SDS), 0.5 M NaPO4, 1 mM EDTA at 50˚C with washing in lx SSC, 0.1% SDS at 50˚C
  • Highly stringent conditions – hybridizes (to the reference nucleotide sequence) in 7% sodium dodecyl sulfate (SDS), 0.5 M NaPO4, 1 mM EDTA at 50˚C with washing in 0.5X SSC, 0.1% SDS at 50˚C (high stringency)
  • Recombinant (nulceic acid) – one produced by human intervention in the nucleotide sequence, typically selection or production

Comments:

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

Scope of independent claim 68 includes bioreporter systems, where the regulatory region of SEQ ID NOs. 13374-17504 may be linked to a polynucleotide coding for a reporter gene, e.g. chloramphenicol acetyl transferase (CAT), beta-glucuronidase (GUS), green fluorescent protein (GFP), beta-galactosidase (beta-GAL), luciferase.
Remarks National phase entry of WO 2003/008540 in Europe (EP 1402042) is pending.

Search strategy

Search details
Date of search 11/05/2006
Database searched Patent Lens
Type of search Expert, stemming on
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.