# Patent

## Title
Shade responsive promoter, promoter control elements, and combinations, and uses thereof

## Abstract

The present invention is directed to promoter sequences and promoter control elements, polynucleotide constructs comprising the promoters and control elements, and methods of identifying the promoters, control elements, or fragments thereof. The invention further relates to the use of the present promoters or promoter control elements to modulate transcript levels.

## Background
This Nonprovisional application claims priority under 35 U.S.C. § 119(e) on U.S. Provisional Application No(s). 60/564,658 and 60/564,678 both filed on Apr. 23, 2004, the entire contents of which are hereby incorporated by reference.


FIELD OF THE INVENTION
The present invention relates to shade responsive promoters and promoter control elements that are useful for modulating transcription of a desired polynucleotide. Such shade responsive promoters and promoter control elements can be included in polynucleotide constructs, expression cassettes, vectors, or inserted into the chromosome or as an exogenous element, to modulate in vivo and in vitro transcription of a polynucleotide. Host cells, including plant cells, and organisms, such as regenerated plants therefrom, with desired traits or characteristics using polynucleotides comprising the shade responsive promoters and promoter control elements of the present invention are also a part of the invention.
BACKGROUND OF THE INVENTION
As every gardener knows, when plants are too close together the crowding elicits a number of developmental responses, such as stem and petiole elongation, branch suppression and accelerated flowering (Smith, H. 1982, Light quality, photoreception and plant strategy. Annu. Rev. Pl. Physiol. 33: 481–518 and Schmitt, J. and R., D., Wulff 1993, Light spectral quality, phytochrome and plant competition. Trends Ecol. Evol. 8:47–50). This shade avoidance response is triggered by the reduced ratio of red to far red wavelengths (R:FR) transmitted through or reflected from green vegetation due to selective absorption of visible wavelengths by chlorophyll (see Smith 1982, above).
It is the phytochrome family of photoreceptors that senses these environmental variations in the R:FR ratio. Phytochromes reversibly switch between R and FR-absorbing forms and interacts with multiple signaling pathways, such as the auxin pathway, to provide a dynamic response to shade (see Smith 1982 and Smith, H. 1995, Physiological and ecological function within the phytochrome family. Annu. Rev. Plant Physiol. Plant Mol. Biol. 46:289–315).
Shade tolerance, or the ability to tolerate extended periods of low light, varies from species to species. Photosynthesis is decreased in shade. As a consequence, in species such as turf grasses this results in decreased carbohydrate reserves and reduced root, rhizome and tiller growth. In the turf grass industry this is problematic because about 20–25% of turf grasses are grown under low light conditions and a considerable amount of time and money is spent by golf courses in an effort to maintain quality turf under shade conditions.
Shade intolerance (shade avoidance) is detrimental to crop plants because the growth and performance of crop plants depends largely on crop architecture, and plant architecture is affected by reduced light. That is, densely planted crops that shade one another tend to place energy into stem and petiole elongation to lift the leaves into the sunlight rather than putting energy into storage or reproductive structures. This negatively affects yields by reducing the amount of harvestable products such as seeds, fruits and tubers. In addition, tall spindly plants tend to be less wind resistant and fall over easily, further reducing crop yield.
Likewise, shade intolerance negatively affects forestry plantings. Here, seedlings of shade tolerate species will self-prune at a slower rate and survive for longer periods under a dense forest canopy than shade intolerant trees. Since most commercially important tree species are shade intolerant to only moderately tolerant of shade, tree plantings must be less dense and require increased acreage.
In the field of agriculture efforts are constantly being made to produce plants with an increased growth potential in order to feed the ever-increasing world population. A similar effort is underway in the field of forestry with the goal of guaranteeing a supply of reproducible raw materials. Conventionally, plant improvement has been achieved via plant breeding. The breeding process is, however, both time-consuming and labor-intensive, especially in forestry where trees may not reach reproductive maturity for decades. Furthermore, appropriate breeding programs must be performed for each relevant plant species.
The genetic manipulation of plants has expedited progress by introducing and expressing specific recombinant nucleic acid molecules. This approach has the advantage of being generally transferable among plant species rather than being limited to one plant species. For example, EP-A 0 511 979 describes the expression of a prokaryotic asparagine synthetase gene in plant cells that leads to increased biomass production. Likewise, WO 96/21737 describes plants with increased yield (growth potential) arising from an increase in the photosynthesis rate and the expression of deregulated or unregulated fructose-1,6-bisphosphatase. Nevertheless, there still is a need for generally applicable processes that improve agricultural and forest plant growth potential. Therefore, the present invention relates to a process for increasing the growth potential in plants, characterized by expression of recombinant DNA molecules stably integrated into the plant genome, particularly in combination with the shade responsive promoters of the invention.
SUMMARY OF THE INVENTION
The present invention is directed to isolated polynucleotide sequences that comprise shade responsive promoters and promoter control elements from plants, especially Arabidopsis thaliana, Glycine max, Oryza sativa, and Zea mays, and other shade responsive promoters and promoter control elements functional in plants.
Plants grown under dense canopies or at high density perceive a decrease in the ratio of red to far-red incoming light, and respond to it by growing faster and taller (Cerdan and Chory, 2003). This can make them feeble in stature and result in seed abortion. Therefore, a further understanding will be important in the appropriate manipulation of a plant's response to shade. One objective of the present invention is to express genes that may attenuate the shade avoidance response when plants sense shaded conditions. To this end, identification of shade induced promoters is extremely valuable.
It is one object of the present invention to provide isolated polynucleotides that are shade responsive promoter sequences. These shade responsive promoter sequences comprise, for example,

    
    
        (1) a polynucleotide having a nucleotide sequence as set forth in the section entitled “The promoter sequence”, and according to SEQ ID NOS. 3–30, or a fragment thereof;
        (2) a polynucleotide having a nucleotide sequence having at least 80% sequence identity to a sequence as set forth in Table 1, in the section entitled “The promoter sequence” or fragment thereof; and
        (3) a polynucleotide having a nucleotide sequence which hybridizes to a sequence as set forth in Table 1, in the section entitled “The promoter sequence” under a condition establishing a Tm −20° C.
    
    


Shade responsive promoter or promoter control element sequences of the present invention are capable of modulating preferential transcription, particularly in response to shade conditions.
In another embodiment, the present shade responsive promoter control elements are capable of serving as or fulfilling the function, for example, as a core shade responsive promoter, a TATA box, a polymerase binding site, an initiator site, a transcription binding site, an enhancer, an inverted repeat, a locus control region, or a scaffold/matrix attachment region.
It is yet another object of the present invention to provide a polynucleotide that includes at least a first and a second promoter control element. The first promoter control element is a promoter control element sequence as discussed above, and the second promoter control element is heterologous to the first control element. Moreover, the first and second control elements are operably linked. Such shade responsive promoters may modulate transcript levels preferentially in a tissue or under particular conditions.
In another embodiment, the present isolated polynucleotide comprises a shade responsive promoter or a promoter control element as described above, wherein the shade responsive promoter or promoter control element is operably linked to a polynucleotide to be transcribed.
In another embodiment of the present vector, the shade responsive promoter and promoter control elements of the instant invention are operably linked to a heterologous polynucleotide that is a regulatory sequence.
It is another object of the present invention to provide a host cell comprising an isolated polynucleotide or vector as described above or fragment thereof. Host cells include, for instance, bacterial, yeast, insect, mammalian, and plant. The host cell can comprise a shade responsive promoter or promoter control element exogenous to the genome. Such a shade responsive promoter can modulate transcription in cis- and in trans-.
In yet another embodiment, the present host cell is a plant cell capable of regenerating into a plant.
It is yet another embodiment of the present invention to provide a plant comprising an isolated polynucleotide or vector described above.
It is another object of the present invention to provide a method of modulating transcription in a sample that contains either a cell-free system of transcription or host cell. This method comprises providing a polynucleotide or vector according to the present invention as described above, and contacting the sample of the polynucleotide or vector with conditions that permit transcription.
In another embodiment of the present method, the polynucleotide or vector preferentially modulates:

    
    
        (a) constitutive transcription,
        (b) stress induced transcription,
        (c) light induced transcription,
        (d) dark induced transcription,
        (e) leaf transcription,
        (f) root transcription,
        (g) stem or shoot transcription,
        (h) silique transcription,
        (i) callus transcription,
        (j) flower transcription,
        (k) immature bud and inflorescence specific transcription, or
        (l) senescing induced transcription
        (m) germination transcription.

Other and further objects of the present invention will be made clear or become apparent from the following description.

    
    





BRIEF DESCRIPTION OF THE TABLES AND FIGURES
FIG. 1 is a schematic representation of the vector pNewBin4-HAP1-GFP.



The definitions of the abbreviations used in the vector map are as follows:

    Ori—the origin of replication used by an E. coli host 
    RB—sequence for the right border of the T-DNA from pMOG800
    BstXI—restriction enzyme cleavage site used for cloning
    HAP1VP16 coding sequence for a fusion protein of the HAP1 and VP16 activation domains
    NOS—terminator region from the nopaline synthase gene
    HAP1UAS—the upstream activating sequence for HAP1
    5ERGFP—the green fluorescent protein gene that has been optimized for localization to the endoplasmic reticulum
    OCS2—the terminator sequence from the octopine synthase 2 gene
    OCS—the terminator sequence from the octopine synthase gene
    p28716 (a.k.a 28716 short) promoter used to drive expression of the PAT (BAR) gene
    PAT (BAR)—a marker gene conferring herbicide resistance
    LB—sequence for the left border of the T-DNA from pMOG800
    Spec—a marker gene conferring spectinomycin resistance
    TrfA—transcription repression factor gene
    RK2-OriV—origin of replication for Agrobacterium


Tables 1 and 2 consist of the Expression Reports for each shade responsive promoter of the invention providing the nucleotide sequence for each shade responsive promoter and details for expression driven by each of the nucleic acid shade responsive promoter sequences as observed in transgenic plants. The results are presented as summaries of the spatial expression, which provides information as to gross and/or specific expression in various plant organs and tissues. The observed expression pattern is also presented, which gives details of expression during different generations or different developmental stages within a generation. Additional information is provided regarding the associated gene, the GenBank reference, the source organism of the promoter, and the vector and marker genes used for the construct. The following symbols are used consistently throughout the Table:

    
    
        T1: First generation transformant
        T2: Second generation transformant
        T3: Third generation transformant
        (L): low expression level
        (M): medium expression level
        (H): high expression level
    
    


Each row of the table begins with a heading identifying the data to be found in the section. The following provides a description of the data to be found in each section:
Description of Table 1











Heading in Table 1
Description







Promoter Candidate ID
Identifies the particular promoter by its construct



ID, including the name of the plant origin.


Modulates the gene as identified by:
This row states the name of the gene modulated by



the promoter


The GenBank description of the gene:
This field gives the Locus Number of the gene as



well as the accession number.


The promoter sequence:
Provides the nucleic acid promoter sequence.


The promoter was cloned from the organism:
Identifies the source of the DNA template used to



clone the promoter.


Alternative nucleotides:
Identifies alternative nucleotides in the promoter



sequence at the base pair positions identified in the



column called “Sequence (bp)” based upon



nucleotide difference between the two species of



Arabidopsis.


The promoter was cloned in the vector:
Identifies the vector used into which a promoter was



cloned.


When cloned into the vector the promoter was
Identifies the type of marker linked to the promoter.


operably linked to a marker, which was the type:
The marker is used to determine patterns of gene



expression in plant tissue.


Promoter-marker vector was tested in:
Identifies the organism in which the promoter-



marker vector was tested.


Generation screened: □T1 Mature □T2
Identifies the plant generation(s) used in the


Seedling □T2 Mature □T3 Seedling
screening process. T1 plants are those plants



subjected to the transformation event while the T2



generation plants are from the seeds collected from



the T1 plants and T3 plants are from the seeds of T2



plants.


The spatial expression of the promoter-marker
Identifies the specific parts of the plant where


vector was found observed in and would be useful in
various levels of GFP expression are observed.


expression in any or all of the following:
Expression levels are noted as either low (L),



medium (M), or high (H).


Observed expression pattern of the promoter-marker
Identifies a general explanation of where GFP


vector was in:
expression in different generations of plants was


T1 mature:
observed.


T2 seedling:


The promoter can be of use in the following trait
Identifies which traits and subtraits the promoter


and sub-trait areas:
cDNA can modulate


The promoter has utility in:
Identifies a specific function or functions that can be



modulated using the promoter cDNA.


Misc. promoter information:
“Bidirectionality” is determined by the number of


Bidirectionality:
base pairs between the promoter and the start codon


Exons:
of a neighboring gene. A promoter is considered


Repeats:
bidirectional if it is closer than 200 bp to a start



codon of a gene 5′ or 3′ to the promoter. “Exons”



(or any coding sequence) identifies if the promoter



has overlapped with either the modulating gene's or



other neighboring gene's coding sequence. A “fail”



for exons means that this overlap has occurred.



“Repeats” identifies the presence of normally



occurring sequence repeats that randomly exist



throughout the genome. A “pass” for repeats



indicates a lack of repeats in the promoter.


Optional Promoter Fragments: An overlap with
Identifies the specific nucleotides overlapping the


the_UTR/exon region of the endogenous coding
UTR region or exon of a neighboring gene. The


sequence to the promoter occurs at base pairs_.
orientation relative to the promoter is designated



with a 5′ or 3′.


The Ceres cDNA ID of the endogenous coding
Identifies the number associated with the Ceres


sequence to the promoter:
cDNA that corresponds to the endogenous cDNA



sequence of the promoter.


cDNA nucleotide sequence:
The nucleic acid sequence of the Ceres cDNA



matching the endogenous cDNA region of the



promoter.


Coding sequence:
A translated protein sequence of the gene modulated



by a protein encoded by a cDNA









Description of Table 2












Heading in Table 2
Description







Promoter Express Report #
Provides an internal report code


Pomoter Tested in
Identified the plant species into which the promoter was



cloved and tested.


Spatial expression summary:
Summarizes the identity of the specific parts of the plant



where various levels of GFP expression was observed.



Expression levels are noted as either Low (L), medium



(M) or high (H).


Observed Expression pattern:
Provides a general explanation of where GFP expression



was observed in different plant generations.


Expected expression patterns:
Identifies tissues where expressions might be expected.


Selection criteria:
Criteria for selecting plants to be observed.


Gene:
Provides information on the closest gene match found in



the Gen Ban and Pfam data bases.


Gen Bank:
Provides information on the closest gene match found in



the Gen Ban and Pfam data bases.


Source Promoter Organism
Identifies the plant source for the cloned promoter.


Vector
Identifies the section into which the promoter was



cloned.


Marker type
The type of marker sequence used.


Generation screened
Identifies the plant generation(s) used in the screening



process. T1 plants are those plants subjected to the



transformation event while the T2 generation plants are



from the seeds collected from the T1 plants and T3



plants are from the seeds of T2 plants.


Inductors completed:
Describes the types of test and general parameters used



for screening of the promoter.


T1 Matures Plant Expression
Reports the observed results of expression in



parts of the plant into L, M, or H being



positioned prior to the name of the observed



tissue.


Promoter Utility:
This section describes a function or functions



that can be modulated using the promoter.


Construct:
This section provides identification numbers



for the promoter and tests.


(A) Predicted promoter sequence:
Provides the sequence information for the



promoter prior to insertion into a plant


(B) Sequence verification and confirmation:
Describes the seqeucne of the promoter as



determined after insertion into a transferred



plant.


(C) Predicted vs. Experimental sequence
Provides an alignment for each of the predicted


experiment
and verified promoter sequences.









The section of Table 1 entitled “optional promoter fragments” identifies the co-ordinates of nucleotides of the promoter that represent optional promoter fragments. The optional promoter fragments comprise the 5′ UTR and any exon(s) of the endogenous coding region. The optional promoter fragments may also comprise any exon(s) and the 3′ or 5′ UTR of the gene residing upstream of the promoter (that is, 5′ to the promoter). The optional promoter fragments also include any intervening sequences that are introns or sequence occurring between exons or an exon and the UTR.
The information on optional promoter fragments can be used to generate either reduced promoter sequences or “core” promoters. A reduced promoter sequence is generated when at least one optional promoter fragment is deleted. Deletion of all optional promoter fragments generates a “core” promoter.
DETAILED DESCRIPTION OF THE INVENTION
1. Definitions
Chimeric: The term “chimeric” is used to describe polynucleotides or genes, as defined supra, or constructs wherein at least two of the elements of the polynucleotide or gene or construct, such as the promoter and the polynucleotide to be transcribed and/or other regulatory sequences and/or filler sequences and/or complements thereof, are heterologous to each other.
Constitutive Promoter: Promoters referred to herein as “constitutive promoters” actively promote transcription under most, but not necessarily all, environmental conditions and states of development or cell differentiation. Examples of constitutive promoters include the cauliflower mosaic virus (CaMV) 35S transcript initiation region and the 1′ or 2′ promoter derived from T-DNA of Agrobacterium tumefaciens, and other transcription initiation regions from various plant genes, such as the maize ubiquitin-1 promoter, known to those of skill.
Core Promoter: This is the minimal stretch of contiguous DNA sequence that is sufficient to direct accurate initiation of transcription by the RNA polymerase II machinery (for review see: Struhl, 1987, Cell 49: 295–297; Smale, 1994, In Transcription: Mechanisms and Regulation (eds R. C. Conaway and J. W. Conaway), pp 63–81/Raven Press, Ltd., New York; Smale, 1997, Biochem. Biophys. Acta 1351:73–88; Smale et al., 1998, Cold Spring Harb. Symp. Quant. Biol. 58: 21–31; Smale, 2001, Genes & Dev. 15: 2503–2508; Weis and Reinberg, 1992, FASEB J. 6: 3300–3309; Burke et al., 1998, Cold Spring Harb. Symp. Quant. Biol 63: 75–82). There are several sequence motifs, including the TATA box, initiator (Inr), TFIIB recognition element (BRE) and downstream core promoter element (DPE), that are commonly found in core promoters, however not all of these elements occur in all promoters and there are no universal core promoter elements (Butler and Kadonaga, 2002, Genes & Dev. 16: 2583–2592).
Domain: Domains are fingerprints or signatures that can be used to characterize protein families and/or parts of proteins. Such fingerprints or signatures can comprise conserved (1) primary sequence, (2) secondary structure, and/or (3) three-dimensional conformation. A similar analysis can be applied to polynucleotides. Generally, each domain has been associated with either a conserved primary sequence or a sequence motif. Generally these conserved primary sequence motifs have been correlated with specific in vitro and/or in vivo activities. A domain can be any length, including the entirety of the polynucleotide to be transcribed. Examples of domains include, without limitation, AP2, helicase, homeobox, zinc finger, etc.
Endogenous: The term “endogenous,” within the context of the current invention refers to any polynucleotide, polypeptide or protein sequence which is a natural part of a cell or organisms regenerated from said cell. In the context of promoter, the term “endogenous coding region” or “endogenous cDNA” refers to the coding region that is naturally operably linked to the promoter.
Enhancer/Suppressor: An “enhancer” is a DNA regulatory element that can increase the steady state level of a transcript, usually by increasing the rate of transcription initiation. Enhancers usually exert their effect regardless of the distance, upstream or downstream location, or orientation of the enhancer relative to the start site of transcription. In contrast, a “suppressor” is a corresponding DNA regulatory element that decreases the steady state level of a transcript, again usually by affecting the rate of transcription initiation. The essential activity of enhancer and suppressor elements is to bind a protein factor(s). Such binding can be assayed, for example, by methods described below. The binding is typically in a manner that influences the steady state level of a transcript in a cell or in an in vitro transcription extract.
Exogenous: As referred to within, “exogenous” is any polynucleotide, polypeptide or protein sequence, whether chimeric or not, that is introduced into the genome of a host cell or orgasm regenerated from said host cell by any means other than by a sexual cross. Examples of means by which this can be accomplished are described below, and include Agrobacterium-mediated transformation (of dicots—e.g. Salomon et al. EMBO J. 3:141 (1984); Herrera-Estrella et al. EMBO J. 2:987 (1983); of monocots, representative papers are those by Escudero et al., Plant J. 10:355 (1996), Ishida et al., Nature Biotechnology 14:745 (1996), May et al., Bio/Technology 13:486 (1995)), biolistic methods (Armaleo et al., Current Genetics 17:97 1990)), electroporation, in planta techniques, and the like. Such a plant containing the exogenous nucleic acid is referred to here as a T0 for the primary transgenic plant and T1 for the first generation. The term “exogenous” as used herein is also intended to encompass inserting a naturally found element into a non-naturally found location.
Gene: The term “gene,” as used in the context of the current invention, encompasses all regulatory and coding sequence contiguously associated with a single hereditary unit with a genetic function (see SCHEMATIC 1). Genes can include non-coding sequences that modulate the genetic function that include, but are not limited to, those that specify polyadenylation, transcriptional regulation, DNA conformation, chromatin conformation, extent and position of base methylation and binding sites of proteins that control all of these. Genes encoding proteins are comprised of “exons” (coding sequences), which may be interrupted by “introns” (non-coding sequences). In some instances complexes of a plurality of protein or nucleic acids or other molecules, or of any two of the above, may be required for a gene's function. On the other hand a gene's genetic function may require only RNA expression or protein production, or may only require binding of proteins and/or nucleic acids without associated expression. In certain cases, genes adjacent to one another may share sequence in such a way that one gene will overlap the other. A gene can be found within the genome of an organism, in an artificial chromosome, in a plasmid, in any other sort of vector, or as a separate isolated entity.
Heterologous sequences: “Heterologous sequences” are those that are not operatively linked or are not contiguous to each other in nature. For example, a promoter from corn is considered heterologous to an Arabidopsis coding region sequence. Also, a promoter from a gene encoding a growth factor from corn is considered heterologous to a sequence encoding the corn receptor for the growth factor. Regulatory element sequences, such as UTRs or 3′ end termination sequences that do not originate in nature from the same gene as the coding sequence originates from, are considered heterologous to said coding sequence. Elements operatively linked in nature and contiguous to each other are not heterologous to each other.
Homologous: In the current invention, a “homologous” gene or polynucleotide or polypeptide refers to a gene or polynucleotide or polypeptide that shares sequence similarity with the gene or polynucleotide or polypeptide of interest. This similarity may be in only a fragment of the sequence and often represents a functional domain such as, examples including without limitation a DNA binding domain or a domain with tyrosine kinase activity. The functional activities of homologous polynucleotide are not necessarily the same.
Inducible Promoter: An “inducible promoter” in the context of the current invention refers to a promoter, the activity of which is influenced by certain conditions, such as light, temperature, chemical concentration, protein concentration, conditions in an organism, cell, or organelle, etc. A typical example of an inducible promoter, which can be utilized with the polynucleotides of the present invention, is PARSK1, the promoter from an Arabidopsis gene encoding a serine-threonine kinase enzyme, and which promoter is induced by dehydration, abscissic acid and sodium chloride (Wang and Goodman, Plant J. 8:37 (1995)). Examples of environmental conditions that may affect transcription by inducible promoters include anaerobic conditions, elevated temperature, the presence or absence of a nutrient or other chemical compound or the presence of light.
Modulate Transcription Level: As used herein, the phrase “modulate transcription” describes the biological activity of a promoter sequence or promoter control element. Such modulation includes, without limitation, includes up- and down-regulation of initiation of transcription, rate of transcription, and/or transcription levels.
Mutant: In the current invention, “mutant” refers to a heritable change in nucleotide sequence at a specific location. Mutant genes of the current invention may or may not have an associated identifiable phenotype.
Operable Linkage: An “operable linkage” is a linkage in which a promoter sequence or promoter control element is connected to a polynucleotide sequence (or sequences) in such a way as to place transcription of the polynucleotide sequence under the influence or control of the promoter or promoter control element. Two DNA sequences (such as a polynucleotide to be transcribed and a promoter sequence linked to the 5′ end of the polynucleotide to be transcribed) are said to be operably linked if induction of promoter function results in the transcription of mRNA encoding the polynucleotide and if the nature of the linkage between the two DNA sequences does not (1) result in the introduction of a frame-shift mutation, (2) interfere with the ability of the promoter sequence to direct the expression of the protein, antisense RNA or ribozyme, or (3) interfere with the ability of the DNA template to be transcribed. Thus, a promoter sequence would be operably linked to a polynucleotide sequence if the promoter was capable of effecting transcription of that polynucleotide sequence.
Optional Promoter Fragments: The phrase “optional promoter fragments” is used to refer to any sub-sequence of the promoter that is not required for driving transcription of an operationally linked coding region. These fragments comprise the 5′ UTR and any exon(s) of the endogenous coding region. The optional promoter fragments may also comprise any exon(s) and the 3′ or 5′ UTR of the gene residing upstream of the promoter (that is, 5′ to the promoter). Optional promoter fragments also include any intervening sequences that are introns or sequence that occurs between exons or an exon and the UTR.
Orthologous: “Orthologous” is a term used herein to describe a relationship between two or more polynucleotides or proteins. Two polynucleotides or proteins are “orthologous” to one another if they serve a similar function in different organisms. In general, orthologous polynucleotides or proteins will have similar catalytic functions (when they encode enzymes) or will serve similar structural functions (when they encode proteins or RNA that form part of the ultrastructure of a cell).
Percentage of sequence identity: “Percentage of sequence identity,” as used herein, is determined by comparing two optimally aligned sequences over a comparison window, where the fragment of the polynucleotide or amino acid sequence in the comparison window may comprise additions or deletions (e.g., gaps or overhangs) as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. The percentage is calculated by determining the number of positions at which the identical nucleic acid base or amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison and multiplying the result by 100 to yield the percentage of sequence identity. Optimal alignment of sequences for comparison may be conducted by the local homology algorithm of Smith and Waterman Add. APL. Math. 2:482 (1981), by the homology alignment algorithm of Needleman and Wunsch J. Mol. Biol. 48:443 (1970), by the search for similarity method of Pearson and Lipman Proc. Natl. Acad. Sci. (USA) 85: 2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, BLAST, PASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group (GCG), 575 Science Dr., Madison, Wis.), or by inspection. Given that two sequences have been identified for comparison, GAP and BESTFIT are preferably employed to determine their optimal alignment. Typically, the default values of 5.00 for gap weight and 0.30 for gap weight length are used.
Plant Promoter: A “plant promoter” is a promoter capable of initiating transcription in plant cells and can modulate transcription of a polynucleotide. Such promoters need not be of plant origin. For example, promoters derived from plant viruses, such as the CaMV35S promoter or from Agrobacterium tumefaciens such as the T-DNA promoters, can be plant promoters. A typical example of a plant promoter of plant origin is the maize ubiquitin-1 (ubi-1) promoter known to those of skill.
Plant Tissue: The term “plant tissue” includes differentiated and undifferentiated tissues or plants, including but not limited to roots, stems, shoots, cotyledons, epicotyl, hypocotyl, leaves, pollen, seeds, tumor tissue and various forms of cells in culture such as single cells, protoplast, embryos, and callus tissue. The plant tissue may be in plants or in organ, tissue or cell culture.
Preferential Transcription: “Preferential transcription” is defined as transcription that occurs in a particular pattern of cell types or developmental times or in response to specific stimuli or combination thereof. Non-limitive examples of preferential transcription include: high transcript levels of a desired sequence in root tissues; detectable transcript levels of a desired sequence in certain cell types during embryogenesis; and low transcript levels of a desired sequence under drought conditions. Such preferential transcription can be determined by measuring initiation, rate, and/or levels of transcription.
Promoter: A “promoter” is a DNA sequence that directs the transcription of a polynucleotide. Typically a promoter is located in the 5′ region of a polynucleotide to be transcribed, proximal to the transcriptional start site of such polynucleotide. More typically, promoters are defined as the region upstream of the first exon; more typically, as a region upstream of the first of multiple transcription start sites; more typically, as the region downstream of the preceding gene and upstream of the first of multiple transcription start sites; more typically, the region downstream of the polyA signal and upstream of the first of multiple transcription start sites; even more typically, about 3,000 nucleotides upstream of the ATG of the first exon; even more typically, 2,000 nucleotides upstream of the first of multiple transcription start sites. The promoters of the invention comprise at least a core promoter as defined above. Frequently promoters are capable of directing transcription of genes located on each of the complementary DNA strands that are 3′ to the promoter. Stated differently, many promoters exhibit bidirectionality and can direct transcription of a downstream gene when present in either orientation (i.e. 5′ to 3′ or 3′ to 5′ relative to the coding region of the gene). Additionally, the promoter may also include at least one control element such as an upstream element. Such elements include UARs and optionally, other DNA sequences that affect transcription of a polynucleotide such as a synthetic upstream element.
Promoter Control Element: The term “promoter control element” as used herein describes elements that influence the activity of the promoter. Promoter control elements include transcriptional regulatory sequence determinants such as, but not limited to, enhancers, scaffold/matrix attachment regions, TATA boxes, transcription start locus control regions, UARs, URRs, other transcription factor binding sites and inverted repeats.
Public sequence: The term “public sequence,” as used in the context of the instant application, refers to any sequence that has been deposited in a publicly accessible database prior to the filing date of the present application. This term encompasses both amino acid and nucleotide sequences. Such sequences are publicly accessible, for example, on the BLAST databases on the NCBI FTP web site (accessible at the National Center for Biotechnology Information (NCBI) website). The database at the NCBI FTP site utilizes “gi” numbers assigned by NCBI as a unique identifier for each sequence in the databases, thereby providing a non-redundant database for sequence from various databases, including GenBank, EMBL, DBBJ, (DNA Database of Japan) and PDB (Brookhaven Protein Data Bank).
Regulatory Sequence: The term “regulatory sequence,” as used in the current invention, refers to any nucleotide sequence that influences transcription or translation initiation and rate, or stability and/or mobility of a transcript or polypeptide product. Regulatory sequences include, but are not limited to, promoters, promoter control elements, protein binding sequences, 5′ and 3′ UTRs, transcriptional start sites, termination sequences, polyadenylation sequences, introns, certain sequences within amino acid coding sequences such as secretory signals, protease cleavage sites, etc.
Related Sequences: “Related sequences” refer to either a polypeptide or a nucleotide sequence that exhibits some degree of sequence similarity with a reference sequence.
Specific Promoters: In the context of the current invention, “specific promoters” refers to a subset of promoters that have a high preference for modulating transcript levels in a specific tissue or organ or cell and/or at a specific time during development of an organism. By “high preference” is meant at least 3-fold, preferably 5-fold, more preferably at least 10-fold still more preferably at least 20-fold, 50-fold or 100-fold increase in transcript levels under the specific condition over the transcription under any other reference condition considered. Typical examples of temporal and/or tissue or organ specific promoters of plant origin that can be used with the polynucleotides of the present invention, are: PTA29, a promoter which is capable of driving gene transcription specifically in tapetum and only during anther development (Koltonow et al., Plant Cell 2:1201 (1990); RCc2 and RCc3, promoters that direct root-specific gene transcription in rice (Xu et al., Plant Mol. Biol. 27:237 (1995); TobRB27, a root-specific promoter from tobacco (Yamamoto et al., Plant Cell 3:371 (1991)). Examples of tissue-specific promoters under developmental control include promoters that initiate transcription only in certain tissues or organs, such as root, ovule, fruit, seeds, or flowers. Other specific promoters include those from genes encoding seed storage proteins or the lipid body membrane protein, oleosin. A few root-specific promoters are noted above. See also “Preferential transcription”.
Stringency: “Stringency” as used herein is a function of probe length, probe composition (G+C content), and salt concentration, organic solvent concentration, and temperature of hybridization or wash conditions. Stringency is typically compared by the parameter Tm, which is the temperature at which 50% of the complementary molecules in the hybridization are hybridized, in terms of a temperature differential from Tm. High stringency conditions are those providing a condition of Tm −5° C. to Tm −10° C. Medium or moderate stringency conditions are those providing Tm −20° C. to Tm −29° C. Low stringency conditions are those providing a condition of Tm −40° C. to Tm −48° C. The relationship of hybridization conditions to Tm (in ° C.) is expressed in the mathematical equation

Tm=81.5−16.6(log10[Na+])+0.41(% G+C)−(600/N)  (1)

where N is the length of the probe. This equation works well for probes 14 to 70 nucleotides in length that are identical to the target sequence. The equation below for Tm of DNA-DNA hybrids is useful for probes in the range of 50 to greater than 500 nucleotides, and for conditions that include an organic solvent (formamide).

Tm=81.5+16.6 log {[Na+]/(1+0.7[Na+])}+0.41(% G+C)−500/L 0.63(% formamide)  (2)

where L is the length of the probe in the hybrid. (P. Tijessen, “Hybridization with Nucleic Acid Probes” in Laboratory Techniques in Biochemistry and Molecular Biology, P. C. vand der Vliet, ed., c. 1993 by Elsevier, Amsterdam.) The Tm of equation (2) is affected by the nature of the hybrid; for DNA-RNA hybrids Tm is 10–15° C. higher than calculated, for RNA-RNA hybrids Tm is 20–25° C. higher. Because the Tm decreases about 1° C. for each 1% decrease in homology when a long probe is used (Bonner et al., J. Mol. Biol. 81:123 (1973)), stringency conditions can be adjusted to favor detection of identical genes or related family members.

Equation (2) is derived assuming equilibrium and therefore, hybridizations according to the present invention are most preferably performed under conditions of probe excess and for sufficient time to achieve equilibrium. The time required to reach equilibrium can be shortened by inclusion of a hybridization accelerator such as dextran sulfate or another high volume polymer in the hybridization buffer.
Stringency can be controlled during the hybridization reaction or after hybridization has occurred by altering the salt and temperature conditions of the wash solutions used. The formulas shown above are equally valid when used to compute the stringency of a wash solution. Preferred wash solution stringencies lie within the ranges stated above; high stringency is 5–8° C. below Tm, medium or moderate stringency is 26–29° C. below Tm and low stringency is 45–48° C. below Tm.
Substantially free of: A composition containing A is “substantially free of” B when at least 85% by weight of the total A+B in the composition is A. Preferably, A comprises at least about 90% by weight of the total of A+B in the composition, more preferably at least about 95% or even 99% by weight. For example, a plant gene can be substantially free of other plant genes. Other examples include, but are not limited to, ligands substantially free of receptors (and vice versa), a growth factor substantially free of other growth factors and a transcription binding factor substantially free of nucleic acids.
Suppressor: See “Enhancer/Suppressor”
TATA to start: “TATA to start” shall mean the distance, in number of nucleotides, between the primary TATA motif and the start of transcription.
Transgenic plant: A “transgenic plant” is a plant having one or more plant cells that contain at least one exogenous polynucleotide introduced by recombinant nucleic acid methods.
Translational start site: In the context of the present invention, a “translational start site” is usually an ATG or AUG in a transcript, often the first ATG or AUG. A single protein encoding transcript, however, may have multiple translational start sites.
Transcription start site: “Transcription start site” is used in the current invention to describe the point at which transcription is initiated. This point is typically located about 25 nucleotides downstream from a TFIID binding site, such as a TATA box. Transcription can initiate at one or more sites within the gene, and a single polynucleotide to be transcribed may have multiple transcriptional start sites, some of which may be specific for transcription in a particular cell-type or tissue or organ. “+1” is stated relative to the transcription start site and indicates the first nucleotide in a transcript.
Upstream Activating Region (UAR): An “Upstream Activating Region” or “UAR” is a position or orientation dependent nucleic acid element that primarily directs tissue, organ, cell type, or environmental regulation of transcript level, usually by affecting the rate of transcription initiation. Corresponding DNA elements that have a transcription inhibitory effect are called herein “Upstream Repressor Regions” or “URR”s. The essential activity of these elements is to bind a protein factor. Such binding can be assayed by methods described below. The binding is typically in a manner that influences the steady state level of a transcript in a cell or in vitro transcription extract.
Untranslated region (UTR): A “UTR” is any contiguous series of nucleotide bases that is transcribed, but is not translated. A 5′ UTR lies between the start site of the transcript and the translation initiation codon and includes the +1 nucleotide. A 3′ UTR lies between the translation termination codon and the end of the transcript. UTRs can have particular functions such as increasing mRNA message stability or translation attenuation. Examples of 3′ UTRs include, but are not limited to polyadenylation signals and transcription termination sequences.
Variant: The term “variant” is used herein to denote a polypeptide or protein or polynucleotide molecule that differs from others of its kind in some way. For example, polypeptide and protein variants can consist of changes in amino acid sequence and/or charge and/or post-translational modifications (such as glycosylation, etc). Likewise, polynucleotide variants can consist of changes that add or delete a specific UTR or exon sequence. It will be understood that there may be sequence variations within sequence or fragments used or disclosed in this application. Preferably, variants will be such that the sequences have at least 80%, preferably at least 90%, 95, 97, 98, or 99% sequence identity. Variants preferably measure the primary biological function of the native polypeptide or protein or polynucleotide.
2. Introduction
The polynucleotides of the invention comprise promoters and promoter control elements that are capable of modulating transcription, particularly in response to shade conditions, thereby enhancing the ability of a plant to grow under such shade conditions.
Such promoters and promoter control elements can be used in combination with native or heterologous promoter fragments, control elements or other regulatory sequences to modulate transcription and/or translation.
Specifically, promoters and control elements of the invention can be used to modulate transcription of a desired polynucleotide, which includes without limitation:

    
    
        (a) antisense;
        (b) ribozymes;
        (c) coding sequences; or
        (d) fragments thereof.

The promoter also can modulate transcription in a host genome in cis- or in trans-.

    
    


In an organism, such as a plant, the promoters and promoter control elements of the instant invention are useful to produce preferential transcription which results in a desired pattern of transcript levels in a particular cells, tissues, or organs, or under particular conditions.
3. Description of the Invention, Experimental Procedures and Results
A. Identifying and Isolating Promoter Sequences of the Invention
The promoters and promoter control elements of the present invention are presented in Tables 1 and 2 in the section entitled “The promoter” sequence in Table 2 in the sections entitled “Predicted promoter sequence” and “Sequence verification and confirmation” and as SEQ ID NOS. 3–30. Additional promoter sequences encompassed by the invention can be identified as described below.
(1) Cloning Methods
Isolation from genomic libraries of polynucleotides comprising the sequences of the promoters and promoter control elements of the present invention is possible using known techniques.
For example, polymerase chain reaction (PCR) can amplify the desired polynucleotides utilizing primers designed from sequences in the row titled “The spatial expression of the promoter-marker-vector”. Polynucleotide libraries comprising genomic sequences can be constructed according to Sambrook et al., Molecular Cloning: A Laboratory Manual, 2nd Ed. (1989) Cold Spring Harbor Press, Cold Spring Harbor, N.Y.), for example.
Other procedures for isolating polynucleotides comprising the promoter sequences of the invention include, without limitation, tail-PCR, and 5′ rapid amplification of cDNA ends (RACE). See, for tail-PCR, for example, Liu et al., Plant J 8(3): 457–463 (September, 1995); Liu et al., Genomics 25: 674–681 (1995); Liu et al., Nucl. Acids Res. 21(14): 3333–3334 (1993); and Zoe et al., BioTechniques 27(2): 240–248 (1999); for RACE, see, for example, PCR Protocols: A Guide to Methods and Applications, (1990) Academic Press, Inc.
(2) Chemical Synthesis
In addition, the promoters and promoter control elements of the invention can be chemically synthesized according to techniques in common use. See, for example, Beaucage et al., Tet. Lett. (1981) 22: 1859 and U.S. Pat. No. 4,668,777.
Such chemical oligonucleotide synthesis can be carried out using commercially available devices, such as, Biosearch 4600 or 8600 DNA synthesizer, by Applied Biosystems, a division of Perkin-Elmer Corp., Foster City, Calif., USA; and Expedite by Perceptive Biosystems, Framingham, Mass., USA.
Synthetic RNA, including natural and/or analog building blocks, can be synthesized on the Biosearch 8600 machines, see above.
Oligonucleotides can be synthesized and then ligated together to construct the desired polynucleotide.
B. Generating Reduced and “Core” Promoter Sequences
Included in the present invention are reduced and “core” promoter sequences. The reduced promoters can be isolated from the promoters of the invention by deleting at least one 5′ UTR, exon or 3′ UTR sequence present in the promoter sequence that is associated with a gene or coding region located 5′ to the promoter sequence or in the promoter's endogenous coding region.
Similarly, the “core” promoter sequences can be generated by deleting all 5′ UTRs, exons and 3′ UTRs present in the promoter sequence and the associated intervening sequences that are related to the gene or coding region 5′ to the promoter region and the promoter's endogenous coding region.
This data is presented in the row titled “Optional Promoter Fragments”.
C. Isolating Related Promoter Sequences
Included in the present invention are promoter and promoter control elements that are related to those described in Table 1 in the section entitled “The promoter sequence”. Such related sequence can be isolated utilizing

    
    
        (a) nucleotide sequence identity;
        (b) coding sequence identity; or
        (c) common function or gene products.

Such related sequences (or “relatives”) can include both naturally occurring promoters and non-natural promoter sequences. Non-natural related promoters include nucleotide substitutions, insertions or deletions of naturally-occurring promoter sequences that do not substantially affect transcription modulation activity. For example, the binding of relevant DNA binding proteins can still occur with the non-natural promoter sequences and promoter control elements of the present invention.

    
    


According to current knowledge, promoter sequences and promoter control elements exist as functionally important regions, such as protein binding sites, and spacer regions. These spacer regions are apparently required for proper positioning of the protein binding sites. Thus, nucleotide substitutions, insertions and deletions can be tolerated in these spacer regions to a certain degree without loss of function.
In contrast, less variation is permissible in the functionally important regions, since changes in the sequence can interfere with protein binding. Nonetheless, some variation in the functionally important regions is permissible so long as function is conserved.
The effects of substitutions, insertions and deletions to the promoter sequences or promoter control elements may be to increase or decrease the binding of relevant DNA binding proteins to modulate transcript levels of a polynucleotide to be transcribed. Effects may include tissue-specific or condition-specific modulation of transcript levels of the polypeptide to be transcribed. Polynucleotides representing changes to the nucleotide sequence of the DNA-protein contact region by insertion of additional nucleotides, changes to identity of relevant nucleotides, including use of chemically-modified bases, or deletion of one or more nucleotides are considered encompassed by the present invention.
(1) Relatives Based on Nucleotide Sequence Identity
Included in the present invention are promoters exhibiting nucleotide sequence identity to those described in Tables 1 and 2 in the section entitled “The promoter sequence”.
Definition
Typically, such related promoters exhibit at least 80% sequence identity, at least 85%, at least 90%, or at least 95%, including, at least 96%, 97%, 98% or 99% sequence identity compared to those shown in Tables 1 and 2 in the section entitled “The promoter” sequence. Such sequence identity can be calculated by the algorithms and computers programs described above.
Usually, such sequence identity is exhibited in an alignment region that is at least 75% of the length of a sequence shown in Tables 1 and 2 in the section entitled “The promoter” sequence or corresponding full-length sequence; more usually at least 80%; more usually, at least 85%, more usually at least 90%, and most usually at least 95%, even more usually, at least 96%, 97%, 98% or 99% of the length of a sequence shown in Tables 1 and 2 in the section entitled “The promoter sequence”.
The percentage of the alignment length is calculated by counting the number of residues of the sequence in region of strongest alignment, e.g., a continuous region of the sequence that contains the greatest number of residues that are identical to the residues between two sequences that are being aligned. The number of residues in the region of strongest alignment is divided by the total residue length of a sequence in Tables 1 and 2 in the section entitled “The promoter sequence”.
These related promoters may exhibit similar preferential transcription as those promoters described in Tables 1 and 2 in the section entitled “The promoter sequence”.
Construction of Polynucleotides
Naturally occurring promoters that exhibit nucleotide sequence identity to those shown in Tables 1 and 2 in the section entitled “The promoter sequence” can be isolated using the techniques as described above. More specifically, such related promoters can be identified by varying stringencies, as defined above, in typical hybridization procedures such as Southern blots or probing of polynucleotide libraries, for example.
Non-natural promoter variants of those shown in Tables 1 and 2 can be constructed using cloning methods that incorporate the desired nucleotide variation. See, for example, Ho, S. N., et al. Gene 77:51–59 1989, describing a procedure site directed mutagenesis using PCR.
Any related promoter showing sequence identity to those shown in Tables 1 and 2 can be chemically synthesized as described above.
Also, the present invention includes non-natural promoters that exhibit the above-sequence identity to those in Tables 1 and 2.
The promoters and promoter control elements of the present invention may also be synthesized with 5′ or 3′ extensions, to facilitate additional manipulation, for instance.
The present invention also includes reduced promoter sequences. These sequences have at least one of the optional promoter fragments deleted.
Core promoter sequences are another embodiment of the present invention. The core promoter sequences have all of the optional promoter fragments deleted.
Testing of Polynucleotides
Polynucleotides of the invention were tested for activity by cloning the sequence into an appropriate vector, transforming plants with the construct and assaying for marker gene expression. Recombinant DNA constructs were prepared which comprise the polynucleotide sequences of the invention inserted into a vector suitable for transformation of plant cells. The construct can be made using standard recombinant DNA techniques (Sambrook et al. 1989) and can be introduced to the species of interest by Agrobacterium-mediated transformation or by other means of transformation as referenced below.
The vector backbone can be any of those typical in the art such as plasmids, viruses, artificial chromosomes, BACs, YACs and PACs and vectors of the sort described by

    (a) BAC: Shizuya et al., Proc. Natl. Acad. Sci. USA 89: 8794–8797 (1992); Hamilton et al., Proc. Natl. Acad. Sci. USA 93: 9975–9979 (1996);
    (b) YAC: Burke et al., Science 236:806–812 (1987);
    (c) PAC: Sternberg N. et al., Proc Natl Acad Sci USA. January; 87(1):103–7 (1990);
    (d) Bacteria-Yeast Shuttle Vectors: Bradshaw et al., Nucl Acids Res 23: 4850–4856 (1995);
    (e) Lambda Phage Vectors: Replacement Vector, e.g., Frischauf et al., J. Mol Biol 170: 827–842 (1983); or Insertion vector, e.g., Huynh et al., In: Glover N.Mex. (ed) DNA Cloning: A practical Approach, Vol. 1 Oxford: IRL Press (1985); T-DNA gene fusion vectors:Walden et al., Mol Cell Biol 1: 175–194 (1990); and
    (g) Plasmid vectors: Sambrook et al., infra.


Typically, the construct comprises a vector containing a sequence of the present invention operationally linked to any marker gene. The polynucleotide was identified as a promoter by the expression of the marker gene. Although many marker genes can be used, Green Fluorescent Protein (GFP) is preferred. The vector may also comprise a marker gene that confers a selectable phenotype on plant cells. The marker may encode biocide resistance, particularly antibiotic resistance, such as resistance to kanamycin, G418, bleomycin, hygromycin, or herbicide resistance, such as resistance to chlorosulfuron or phosphinotricin. Vectors can also include origins of replication, scaffold attachment regions (SARs), markers, homologous sequences, introns, etc.
Promoter Control Elements of the Invention
The promoter control elements of the present invention include those that comprise a sequence shown in Tables 1 and 2 in the section entitled “The promoter sequence” and those that comprise fragments of SEQ ID NOS. 3–30, but that still possess shade responsive activity. The size of the fragments can range from 5 bases to 10 kilobases (kb). Typically, the fragment size is no smaller than 8 bases; more typically, no smaller than 12; more typically, no smaller than 15 bases; more typically, no smaller than 20 bases; more typically, no smaller than 25 bases; even more typically, no more than 30, 35, 40 or 50 bases.
Usually, the fragment size in no larger than 5 kb bases; more usually, no larger than 2 kb; more usually, no larger than 1 kb; more usually, no larger than 800 bases; more usually, no larger than 500 bases; even more usually, no more than 250, 200, 150 or 100 bases.
Relatives Based on Nucleotide Sequence Identity
Included in the present invention are promoter control elements exhibiting nucleotide sequence identity to those described in Tables 1 and 2 in the section entitled “The promoter sequence” of fragments thereof.
Typically, such related promoters exhibit at least 80% sequence identity, preferably at least 85%, more preferably at least 90%, and most preferably at least 95%, even more preferably, at least 96%, 97%, 98% or 99% sequence identity compared to those shown in Tables 1 and 2 in the section entitled “The promoter sequence”. Such sequence identity can be calculated by the algorithms and computers programs described above.
Promoter Motifs of the Invention
The promoter motifs of the present invention include those that comprise a sequence shown in Tables 1 and 2 in the section entitled “The promoter sequence” and those that comprise fragments of SEQ ID NOS. 3–30, but that still possess nitrogen responsive activity. The size of the motif can range from 2 bases to 500 bases. Typically, the motif size is no smaller than 3 bases; more typically, no smaller than 4; even more typically, no smaller than 5, 6, 7, 8, 9 or 10 bases.
Usually, the motif size is no longer than 500 bases; more longer than 40 bases; more usually, no larger than 30 bases; even more usually, no more than 25, 20 or 15 bases.
Promoter Control Element Configuration
Promoters are generally modular in nature. Promoters can consist of a basal promoter which functions as a site for assembly of a transcription complex comprising an RNA polymerase, for example RNA polymerase II. A typical transcription complex will include additional factors such as TFIIB, TFIID, and TFIIE. Of these, TFIID appears to be the only one to bind DNA directly. The promoter might also contain one or more promoter control elements such as the elements discussed above. These additional control elements may function as binding sites for additional transcription factors that have the function of modulating the level of transcription with respect to tissue specificity and of transcriptional responses to particular environmental or nutritional factors, and the like.
One type of promoter control element is a polynucleotide sequence representing a binding site for proteins. Typically, within a particular functional module, protein binding sites constitute regions of 5 to 60, preferably 10 to 30, more preferably 10 to 20 nucleotides. Within such binding sites, there are typically 2 to 6 nucleotides which specifically contact amino acids of the nucleic acid binding protein.
The protein binding sites are usually separated from each other by 10 to several hundred nucleotides, typically by 15 to 150 nucleotides, often by 20 to 50 nucleotides.
Further, protein binding sites in promoter control elements often display dyad symmetry in their sequence. Such elements can bind several different proteins, and/or a plurality of sites can bind the same protein. Both types of elements may be combined in a region of 50 to 1,000 base pairs.
Binding sites for any specific factor have been known to occur almost anywhere in a promoter. For example, functional AP-1 binding sites can be located far upstream, as in the rat bone sialoprotein gene, where an AP-1 site located about 900 nucleotides upstream of the transcription start site suppresses expression. Yamauchi et al., Matrix Biol., 15, 119–130 (1996). Alternatively, an AP-1 site located close to the transcription start site plays an important role in the expression of Moloney murine leukemia virus. Sap et al., Nature, 340, 242–244, (1989).
D. Constructing Promoters with Control Elements
(1) Combining Promoters and Promoter Control Elements
The promoter polynucleotides and promoter control elements of the present invention, both naturally occurring and synthetic, can be combined with each other to produce the desired preferential transcription. Also, the polynucleotides of the invention can be combined with other known sequences to obtain other useful promoters to modulate, for example, tissue transcription specific or transcription specific to certain conditions. Such preferential transcription can be determined using the techniques or assays described above.
Fragments, variants, as well as full-length sequences those shown in Tables 1 and 2 in the section entitled “The promoter sequence” and relatives are useful alone or in combination.
The location and relation of promoter control elements within a promoter can affect the ability of the promoter to modulate transcription. The order and spacing of control elements is a factor when constructing promoters.
(2) Number of Promoter Control Elements
Promoters can contain any number of control elements. For example, a promoter can contain multiple transcription binding sites or other control elements. One element may confer tissue or organ specificity; another element may limit transcription to specific time periods, etc. Typically, promoters will contain at least a basal or core promoter as described above. Any additional element can be included as desired. For example, a fragment comprising a basal or “core” promoter can be fused with another fragment with any number of additional control elements.
(3) Spacing Between Control Elements
Spacing between control elements or the configuration or control elements can be determined or optimized to permit the desired protein-polynucleotide or polynucleotide interactions to occur.
For example, if two transcription factors bind to a promoter simultaneously or relatively close in time, the binding sites are spaced to allow each factor to bind without steric hindrance. The spacing between two such hybridizing control elements can be as small as a profile of a protein bound to a control element. In some cases, two protein binding sites can be adjacent to each other when the proteins bind at different times during the transcription process.
Further, when two control elements hybridize the spacing between such elements will be sufficient to allow the promoter polynucleotide to hairpin or loop to permit the two elements to bind. The spacing between two such hybridizing control elements can be as small as a t-RNA loop, to as large as 10 kb.
Typically, the spacing is no smaller than 5 bases; more typically, no smaller than 8; more typically, no smaller than 15 bases; more typically, no smaller than 20 bases; more typically, no smaller than 25 bases; even more typically, no more than 30, 35, 40 or 50 bases.
Usually, the fragment size in no larger than 5 kb bases; more usually, no larger than 2 kb; more usually, no larger than 1 kb; more usually, no larger than 800 bases; more usually, no larger than 500 bases; even more usually, no more than 250, 200, 150 or 100 bases.
Such spacing between promoter control elements can be determined using the techniques and assays described above.
(4) Other Promoters
The shade responsive promoters, promoter control elements and motifs of the present invention can be combined in a construct with other known promoters to effect transcription in a desired manner. The following are promoters that are induced under stress conditions and can be combined with those of the present invention: 1dh1 (oxygen stress; tomato; see Germain and Ricard. 1997. Plant Mol Biol 35:949–54), GPx and CAT (oxygen stress; mouse; see Franco et al. 1999. Free Radic Biol Med 27:1122–32), ci7 (cold stress; potato; see Kirch et al. 1997. Plant Mol Biol. 33:897–909), Bz2 (heavy metals; maize; see Marrs and Walbot. 1997. Plant Physiol 113:93–102), HSP32 (hyperthermia; rat; see Raju and Maines. 1994. Biochem Biophys Acta 1217:273–80); MAPKAPK-2 (heat shock; Drosophila; see Larochelle and Suter. 1995. Gene 163:209–14).
In addition, the following examples of promoters are induced by the presence or absence of light can be used in combination with those of the present invention: Topoisomerase II (pea; see Reddy et al. 1999. Plant Mol Biol 41:125–37), chalcone synthase (soybean; see Wingender et al. 1989. Mol Gen Genet 218:315–22) mdm2 gene (human tumor; see Saucedo et al. 1998. Cell Growth Differ 9:119–30), Clock and BMAL1 (rat; see Namihira et al. 1999. Neurosci Lett 271:1–4, PHYA (Arabidopsis; see Canton and Quail 1999. Plant Physiol 121:1207–16), PRB-1b (tobacco; see Sessa et al. 1995. Plant Mol Biol 28:537–47) and Ypr10 (common bean; see Walter et al. 1996. Eur J Biochem 239:281–93).
The promoters and control elements of the following genes can be used in combination with the present invention to confer tissue specificity: MipB (iceplant; Yamada et al. 1995. Plant Cell 7:1129–42) and SUCS (root nodules; broadbean; Kuster et al. 1993. Mol Plant Microbe Interact 6:507–14) for roots, OsSUT1 (rice; Hirose et al. 1997. Plant Cell Physiol 38:1389–96) for leaves, Msg (soybean; Stomvik et al. 1999. Plant Mol Biol 41:217–31) for siliques, cell (Arabidopsis; Shani et al. 1997. Plant Mol Biol 34(6):837–42) and ACT11 (Arabidopsis; Huang et al. 1997. Plant Mol Biol 33:125–39) for inflorescence.
Still other promoters are affected by hormones or participate in specific physiological processes, which can be used in combination with those of present invention. Some examples are the ACC synthase gene that is induced differently by ethylene and brassinosteroids (mung bean; Yi et al. 1999. Plant Mol Biol41:443–54), the TAPG1 gene that is active during abscission (tomato; Kalaitzis et al. 1995. Plant Mol Biol 28:647–56), and the 1-aminocyclopropane-1-carboxylate synthase gene (carnation; Jones et al. 19951 Plant Mol Biol 28:505–12) and the CP-2/cathepsin L gene (rat; Kim and Wright. 1997. Biol Reprod 57:1467–77), both active during senescence.
E. Vectors
Vectors are a useful component of the present invention. In particular, the present promoters and/or promoter control elements may be delivered to a system such as a cell by way of a vector. For the purposes of this invention, such delivery may range from simply introducing the promoter or promoter control element by itself randomly into a cell to integration of a cloning vector containing the present promoter or promoter control element. Thus, a vector need not be limited to a DNA molecule such as a plasmid, cosmid or bacterial phage that has the capability of replicating autonomously in a host cell. All other manner of delivery of the promoters and promoter control elements of the invention are envisioned. The various T-DNA vector types are a preferred vector for use with the present invention. Many useful vectors are commercially available.
It may also be useful to attach a marker sequence to the present promoter and promoter control element in order to determine activity of such sequences. Marker sequences typically include genes that provide antibiotic resistance, such as tetracycline resistance, hygromycin resistance or ampicillin resistance, or provide herbicide resistance. Specific selectable marker genes may be used to confer resistance to herbicides such as glyphosate, glufosinate or broxynil (Comai et al., Nature 317: 741–744 (1985); Gordon-Kamm et al., Plant Cell 2: 603–618 (1990); and Stalker et al., Science 242: 419–423 (1988)). Other marker genes exist which provide hormone responsiveness.
(1) Modification of Transcription by Promoters and Promoter Control Elements
The promoter or promoter control element of the present invention may be operably linked to a polynucleotide to be transcribed. In this manner, the promoter or promoter control element may modify-transcription by modulate transcript levels of that polynucleotide when inserted into a genome.
However, prior to insertion into a genome, the promoter or promoter control element need not be linked, operably or otherwise, to a polynucleotide to be transcribed. For example, the promoter or promoter control element may be inserted alone into the genome in front of a polynucleotide already present in the genome. In this manner, the promoter or promoter control element may modulate the transcription of a polynucleotide that was already present in the genome. This polynucleotide may be native to the genome or inserted at an earlier time.
Alternatively, the promoter or promoter control element may be inserted into a genome alone to modulate transcription. See, for examples Vaucheret, H et al. (1998) Plant J 16: 651–659. The promoter or promoter control element may be simply inserted into a genome or maintained extrachromosomally as a way to divert transcription resources of the system to itself. This approach may be used to down regulate the transcript levels of a group of polynucleotide(s).
(2) Polynucleotide to be Transcribed
The nature of the polynucleotide to be transcribed is not limited. Specifically, the polynucleotide may include sequences that will have activity as RNA as well as sequences that result in a polypeptide product. These sequences may include, but are not limited to antisense sequences, ribozyme sequences, spliceosomes, amino acid coding sequences, and fragments thereof.
Specific coding sequences may include, but are not limited to endogenous proteins or fragments thereof, or heterologous proteins including marker genes or fragments thereof.
Promoters and control elements of the present invention are useful for modulating metabolic or catabolic processes. Such processes include, but are not limited to, secondary product metabolism, amino acid synthesis, seed protein storage, oil development, pest defense and nitrogen usage. Some examples of genes, transcripts and peptides or polypeptides participating in these processes, which can be modulated by the present invention: are tryptophan decarboxylase (tdc) and strictosidine synthase (str1), dihydrodipicolinate synthase (DHDPS) and aspartate kinase (AK), 2S albumin and alpha-, beta-, and gamma-zeins, ricinoleate and 3-ketoacyl-ACP synthase (KAS), Bacillus thuringiensis (Bt) insecticidal protein, cowpea trypsin inhibitor (CpTI), asparagine synthetase and nitrite reductase. Alternatively, expression constructs can be used to inhibit expression of these peptides and polypeptides by incorporating the promoters in constructs for antisense use, co-suppression use or for the production of dominant negative mutations.
(3) Other Regulatory Elements
As explained above, several types of regulatory elements exist concerning transcription regulation. Each of these regulatory elements may be combined with the present vector if desired.
(4) Other Components of Vectors
Translation of eukaryotic mRNA is often initiated at the codon that encodes the first methionine. Thus, when constructing a recombinant polynucleotide according to the present invention for expressing a protein product, it is preferable to ensure that the linkage between the 3′ portion, preferably including the TATA box, of the promoter and the polynucleotide to be transcribed, or a functional derivative thereof, does not contain any intervening codons which are capable of encoding a methionine.
The vector of the present invention may contain additional components. For example, an origin of replication allows for replication of the vector in a host cell. Additionally, homologous sequences flanking a specific sequence allows for specific recombination of the specific sequence at a desired location in the target genome. T-DNA sequences also allow for insertion of a specific sequence randomly into a target genome.
The vector may also be provided with a plurality of restriction sites for insertion of a polynucleotide to be transcribed as well as the promoter and/or promoter control elements of the present invention. The vector may additionally contain selectable marker genes. The vector may also contain a transcriptional and translational initiation region, and a transcriptional and translational termination region functional in the host cell. The termination region may be native with the transcriptional initiation region, may be native with the polynucleotide to be transcribed, or may be derived from another source. Convenient termination regions are available from the Ti-plasmid of A. tumefaciens, such as the octopine synthase and nopaline synthase termination regions. See also, Guerineau et al., (1991) Mol. Gen. Genet. 262:141–144; Proudfoot (1991) Cell 64:671–674; Sanfacon et al. (1991) Genes Dev. 5:141–149; Mogen et al. (1990) Plant Cell 2:1261–1272; Munroe et al. (1990) Gene 91:151–158; Ballas et al. 1989) Nucleic Acids Res. 17:7891–7903; Joshi et al. (1987) Nucleic Acid Res. 15:9627–9639.
Where appropriate, the polynucleotide to be transcribed may be optimized for increased expression in a certain host cell. For example, the polynucleotide can be synthesized using preferred codons for improved transcription and translation. See U.S. Pat. Nos. 5,380,831, 5,436,391; see also and Murray et al., (1989) Nucleic Acids Res. 17:477–498.
Additional sequence modifications include elimination of sequences encoding spurious polyadenylation signals, exon intron splice site signals, transposon-like repeats, and other such sequences well characterized as deleterious to expression. The G-C content of the polynucleotide may be adjusted to levels average for a given cellular host, as calculated by reference to known genes expressed in the host cell. The polynucleotide sequence may be modified to avoid hairpin secondary mRNA structures.
A general description of expression vectors and reporter genes can be found in Gruber, et al., “Vectors for Plant Transformation, in Methods in Plant Molecular Biology & Biotechnology” in Glich et al., (Eds. pp. 89–119, CRC Press, 1993). Moreover GUS expression vectors and GUS gene cassettes are available from Clonetech Laboratories, Inc., Palo Alto, Calif. while luciferase expression vectors and luciferase gene cassettes are available from Promega Corp. (Madison, Wis.). GFP vectors are available from Aurora Biosciences.
F. Polynucleotide Insertion Into A Host Cell
The polynucleotides according to the present invention can be inserted into a host cell. A host cell includes but is not limited to a plant, mammalian, insect, yeast, and prokaryotic cell, preferably a plant cell.
The method of insertion into the host cell genome is chosen based on convenience. For example, the insertion into the host cell genome may either be accomplished by vectors that integrate into the host cell genome or by vectors which exist independent of the host cell genome.
(1) Polynucleotides Autonomous of the Host Genome
The polynucleotides of the present invention can exist autonomously or independent of the host cell genome. Vectors of these types are known in the art and include, for example, certain type of non-integrating viral vectors, autonomously replicating plasmids, artificial chromosomes, and the like.
Additionally, in some cases transient expression of a polynucleotide may be desired.
(2) Polynucleotides Integrated into the Host Genome
The promoter sequences, promoter control elements or vectors of the present invention may be transformed into host cells. These transformations may be into protoplasts or intact tissues or isolated cells. Preferably expression vectors are introduced into intact tissue. General methods of culturing plant tissues are provided for example by Maki et al. “Procedures for Introducing Foreign DNA into Plants” in Methods in Plant Molecular Biology & Biotechnology, Glich et al. (Eds. pp. 67–88 CRC Press, 1993); and by Phillips et al. “Cell-Tissue Culture and In-Vitro Manipulation” in Corn & Corn Improvement, 3rd Edition 10 Sprague et al. (Eds. pp. 345–387) American Society of Agronomy Inc. et al. 1988.
Methods of introducing polynucleotides into plant tissue include the direct infection or co-cultivation of plant cell with Agrobacterium tumefaciens, Horsch et al., Science, 227:1229 (1985). Descriptions of Agrobacterium vector systems and methods for Agrobacterium-mediated gene transfer provided by Gruber et al. supra.
Alternatively, polynucleotides are introduced into plant cells or other plant tissues using a direct gene transfer method such as microprojectile-mediated delivery, DNA injection, electroporation and the like. More preferably polynucleotides are introduced into plant tissues using the microprojectile media delivery with the biolistic device. See, for example, Tomes et al., “Direct DNA transfer into intact plant cells via microprojectile bombardment” In: Gamborg and Phillips (Eds.) Plant Cell, Tissue and Organ Culture: Fundamental Methods, Springer Verlag, Berlin (1995).
In another embodiment of the current invention, expression constructs can be used for gene expression in callus culture for the purpose of expressing marker genes encoding peptides or polypeptides that allow identification of transformed plants. Here, a promoter that is operatively linked to a polynucleotide to be transcribed is transformed into plant cells and the transformed tissue is then placed on callus-inducing media. If the transformation is conducted with leaf discs, for example, callus will initiate along the cut edges. Once callus growth has initiated, callus cells can be transferred to callus shoot-inducing or callus root-inducing media. Gene expression will occur in the callus cells developing on the appropriate media: callus root-inducing promoters will be activated on callus root-inducing media, etc. Examples of such peptides or polypeptides useful as transformation markers include, but are not limited to barstar, glyphosate, chloramphenicol acetyltransferase (CAT), kanamycin, spectinomycin, streptomycin or other antibiotic resistance enzymes, green fluorescent protein (GFP), and β-glucuronidase (GUS), etc. Some of the exemplary promoters of the row titled “The promoter sequence” will also be capable of sustaining expression in some tissues or organs after the initiation or completion of regeneration. Examples of these tissues or organs are somatic embryos, cotyledon, hypocotyl, epicotyl, leaf, stems, roots, flowers and seed.
Integration into the host cell genome also can be accomplished by methods known in the art, for example, by the homologous sequences or T-DNA discussed above or using the cre-lox system (A. C. Vergunst et al., Plant Mol. Biol. 38:393 (1998)).
G. Using the Promoters of the Invention
Common Uses
In yet another embodiment, the promoters of the present invention can be used to further understand developmental mechanisms. For example, shade responsive promoters that are specifically induced during callus formation, somatic embryo formation, shoot formation or root formation can be used to explore the effects of over expression, repression or ectopic expression of target genes, or for isolation of trans-acting factors.
The vectors of the invention can be used not only for expression of coding regions but may also be used in exon-trap cloning, or promoter trap procedures to detect differential gene expression in various tissues, K. Lindsey et al., 1993 “Tagging Genomic Sequences That Direct Transgene Expression by Activation of a Promoter Trap in Plants”, Transgenic Research 2:3347. D. Auch & Reth, et al., “Exon Trap Cloning: Using PCR to Rapidly Detect and Clone Exons from Genomic DNA Fragments”, Nucleic Acids Research, Vol. 18, No. 22, p. 674.
Entrapment vectors, first described for use in bacteria (Casadaban and Cohen, 1979, Proc. Nat. Aca. Sci. U.S.A., 76: 4530; Casadaban et al., 1980, J. Bacteriol., 143: 971) permit selection of insertional events that lie within coding sequences. Entrapment vectors can be introduced into pluripotent ES cells in culture and then passed into the germline via chimeras (Gossler et al., 1989, Science, 244: 463; Skames, 1990, Biotechnology, 8: 827). Promoter or gene trap vectors often contain a reporter gene, e.g., lacZ, lacking its own promoter and/or splice acceptor sequence upstream. That is, promoter gene traps contain a reporter gene with a splice site but no promoter. If the vector lands in a gene and is spliced into the gene product, then the reporter gene is expressed.
Recently, the isolation of preferentially-induced genes has been made possible with the use of sophisticated promoter traps (e.g. IVET) that are based on conditional auxotrophy complementation or drug resistance. In one IVET approach, various bacterial genome fragments are placed in front of a necessary metabolic gene coupled to a reporter gene. The DNA constructs are inserted into a bacterial strain otherwise lacking the metabolic gene, and the resulting bacteria are used to infect the host organism. Only bacteria expressing the metabolic gene survive in the host organism; consequently, inactive constructs can be eliminated by harvesting only bacteria that survive for some minimum period in the host. At the same time, constitutively active constructs can be eliminated by screening only bacteria that do not express the reporter gene under laboratory conditions. The bacteria selected by such a method contain constructs that are selectively induced only during infection of the host. The IVET approach can be modified for use in plants to identify genes induced in either the bacteria or the plant cells upon pathogen infection or root colonization. For information on IVET see the articles by Mahan et al. in Science 259:686–688 (1993), Mahan et al. in PNAS USA 92:669–673 (1995), Heithoff et al. in PNAS USA 94:934–939 (1997), and Wanget al. in PNAS USA. 93:10434 (1996).
Constitutive Transcription
Use of promoters and control elements providing constitutive transcription is desired for modulation of transcription in most cells of an organism under most environmental conditions. In a plant, for example, constitutive transcription is useful for modulating genes involved in defense, pest resistance, herbicide resistance, etc.
Constitutive up-regulation and transcription down-regulation is useful for these applications. For instance, genes, transcripts, and/or polypeptides that increase defense, pest and herbicide resistance may require constitutive up-regulation of transcription. In contrast, constitutive transcriptional down-regulation may be desired to inhibit those genes, transcripts, and/or polypeptides that lower defense, pest and herbicide resistance.
Typically, promoter or control elements that provide constitutive transcription produce transcription levels that are statistically similar in many tissues and environmental conditions observed.
Calculation of P-value from the different observed transcript levels is one means of determining whether a promoter or control element is providing constitutive up-regulation. P-value is the probability that the difference of transcript levels is not statistically significant. The higher the P-value, the more likely the difference of transcript levels is not significant. One formula used to calculate P-value is as follows:



  
    
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The P-value from the formula ranges from 1.0 to 0.0.

Usually, each P-value of the transcript levels observed in a majority of cells, tissues, or organs under various environmental conditions produced by the promoter or control element is greater than 10−8; more usually, greater than 10−7; even more usually, greater than 10−6; even more usually, greater than 10−5 or 10−4.
For up-regulation of transcription, promoter and control elements produce transcript levels that are above background of the assay.
Dark or Shade Induced Preferential Transcription
Promoters and control elements providing preferential transcription when induced by dark or decreased light intensity (shade) or decreased light exposure time can be utilized to time growth, metabolism, and development, to modulate photosynthesis capabilities for host cells or, organisms. In a plant, for example, modulation of genes, transcripts, and/or polypeptides in response to dark is useful, for example,

    
    
        (1) to induce growth or development, such as fruit development and maturity, despite lack of light;
        (2) to modulate genes, transcripts, and/or polypeptide active at night or on cloudy days; or
        (3) to preserve the plastid ultra structure present at the onset of darkness.

The present promoters and control elements can also trigger response similar to those described in the section above.

    
    


Up-regulation and transcription down-regulation is useful for these applications. For instance, genes, transcripts, and/or polypeptides that increase growth and development may require up-regulation of transcription. In contrast, transcriptional down-regulation may be desired to inhibit those genes, transcripts, and/or polypeptides that modulate photosynthesis capabilities.
Typically, promoter or control elements, which provide preferential transcription under exposure to dark or decrease light intensity or decrease exposure time, produce transcript levels that are statistically significant.
For preferential up-regulation of transcription, promoter and control elements produce transcript levels that are above background of the assay.
GFP Experimental Procedures and Results
Procedures
The polynucleotide sequences of the present invention were tested for promoter activity using Green Fluorescent Protein (GFP) assays in one of the following manner.
A. Shade Cloth Procedure
Approximately 1–2 kb of genomic sequence occurring immediately upstream of the ATG translational start site of the gene of interest was isolated using appropriate primers tailed with BstXI restriction sites. Standard PCR reactions using these primers and genomic DNA were conducted. The resulting product was isolated, cleaved with BstXI and cloned into the BstXI site of an appropriate vector, such as pNewBin4-HAP1-GFP (see FIG. 1).
Transformation
The following procedure was used for transformation of plants
1. Stratification of WS-2 Seed.


    
    
        Add 0.5 ml WS-2 (CS2360) seed to 50 ml of 0.2% Phytagar in a 50 ml Corning tube and vortex until seeds and Phytagar form a homogenous mixture.
        Cover tube with foil and stratify at 4° C. for 3 days.

2. Preparation of Seed Mixture.

        Obtain stratified seed from cooler.
        Add seed mixture to a 1000 ml beaker.
        Add an additional 950 ml of 0.2% Phytagar and mix to homogenize.

3. Preparation of Soil Mixture.

        Mix 24 L SunshineMix #5 soil with 16 L Therm-O-Rock vermiculite in cement mixer to make a 60:40 soil mixture.
        Amend soil mixture by adding 2 Tbsp Marathon and 3 Tbsp Osmocote and mix contents thoroughly.
        Add 1 Tbsp Peters fertilizer to 3 gallons of water and add to soil mixture and mix thoroughly.
        Fill 4-inch pots with soil mixture and round the surface to create a slight dome.
        Cover pots with 8-inch squares of nylon netting and fasten using rubber bands.
        Place 14 4-inch pots into each no-hole utility flat.

4. Planting.

        Using a 60 ml syringe, aspirate 35 ml of the seed mixture.
        Exude 25 drops of the seed mixture onto each pot.
        Repeat until all pots have been seeded.
        Place flats on greenhouse bench, cover flat with clear propagation domes, place 55% shade cloth on top of flats and subirrigate by adding 1 inch of water to bottom of each flat.

5. Plant Maintenance.

        3 to 4 days after planting, remove clear lids and shade cloth.
        Subirrigate flats with water as needed.
        After 7–10 days, thin pots to 20 plants per pot using forceps.
        After 2 weeks, subirrigate all plants with Peters fertilizer at a rate of 1 Tsp per gallon water.
        When bolts are about 5–10 cm long, clip them between the first node and the base of stem to induce secondary bolts.
        6 to 7 days after clipping, perform dipping infiltration.

6. Preparation of Agrobacterium. 

        Add 150 ml fresh YEB to 250 ml centrifuge bottles and cap each with a foam plug (IdentiPlug).
        Autoclave for 40 min at 121° C.
        After cooling to room temperature, uncap and add 0.1 ml each of carbenicillin, spectinomycin and rifampicin stock solutions to each culture vessel.
        Obtain Agrobacterium starter block (96-well block with Agrobacterium cultures grown to an OD600 of approximately 1.0) and inoculate one culture vessel per construct by transferring 1 ml from appropriate well in the starter block.
        Cap culture vessels and place on Lab-Line incubator shaker set at 27° C. and 250 RPM.
        Remove after Agrobacterium cultures reach an OD600 of approximately 1.0 (about 24 hours), cap culture vessels with plastic caps, place in Sorvall SLA 1500 rotor and centrifuge at 8000 RPM for 8 min at 4° C.
        Pour out supernatant and put bottles on ice until ready to use.
        Add 200 ml Infiltration Media (IM) to each bottle, resuspend Agrobacterium pellets and store on ice.

7. Dipping Infiltration.

        Pour resuspended Agrobacterium into 16 oz polypropylene containers.
        Invert 4-inch pots and submerge the aerial portion of the plants into the Agrobacterium suspension and let stand for 5 min.
        Pour out Agrobacterium suspension into waste bucket while keeping polypropylene container in place and return the plants to the upright position.
        Place 10 covered pots per flat.
        Fill each flat with 1-inch of water and cover with shade cloth.
        Keep covered for 24 hr and then remove shade cloth and polypropylene containers.
        Resume normal plant maintenance.
        When plants have finished flowering cover each pot with a ciber plant sleeve.
        After plants are completely dry, collect seed and place into 2.0 ml micro tubes and store in 100-place cryogenic boxes.

Recipes:

0.2% Phytagar

        2 g Phytagar
        1 L nanopure water
        
            Shake until Phytagar suspended
            Autoclave 20 min

YEB (for 1 L)

        
        
        5 g extract of meat
        5 g Bacto peptone
        1 g yeast extract
        5 g sucrose
        
            0.24 g magnesium sulfate
            While stirring, add ingredients, in order, to 900 ml nanopure water
            When dissolved, adjust pH to 7.2
            Fill to 1 L with nanopure water
            Autoclave 35 min

Infiltration Medium (IM) (for 1 L)

        
        
        2.2 g MS salts
        50 g sucrose
        5 ul BAP solution (stock is 2 mg/ml)
        
            While stirring, add ingredients in order listed to 900 ml nanopure water
            When dissolved, adjust pH to 5.8.
            Volume up to 1 L with nanopure water.
            Add 0.02% Silwet L-77 just prior to resuspending Agrobacterium 

High Throughput Screening—T1 Generation

1. Soil Preparation. Wear gloves at all times.

        
        
        In a large container, mix 60% autoclaved SunshineMix #5 with 40% vermiculite.
        Add 2.5 Tbsp of Osmocote, and 2.5 Tbsp of 1% granular Marathon per 25 L of soil.
        Mix thoroughly.

2. Fill Com-Packs With Soil.

        Loosely fill D601 Com-Packs level to the rim with the prepared soil.
        Place filled pot into utility flat with holes, within a no-hole utility flat.
        Repeat as necessary for planting. One flat set should contain 6 pots.

3. Saturate Soil.

        Evenly water all pots until the soil is saturated and water is collecting in the bottom of the flats.
        After the soil is completely saturated, dump out the excess water.

4. Plant the Seed.

5. Stratify the Seeds.

        After sowing the seed for all the flats, place them into a dark 4° C. cooler.
        Keep the flats in the cooler for 2 nights for WS seed. Other ecotypes may take longer.
        This cold treatment will help promote uniform germination of the seed.

6. Remove Flats From Cooler and Cover With Shade Cloth. (Shade cloth is only needed in the greenhouse)

        After the appropriate time, remove the flats from the cooler and place onto growth racks or benches.
        Cover the entire set of flats with 55% shade cloth. The cloth is necessary to cut down the light intensity during the delicate germination period.
        The cloth and domes should remain on the flats until the cotyledons have fully expanded. This usually takes about 4–5 days under standard greenhouse conditions.

7. Remove 55% Shade Cloth and Propagation Domes.

        After the cotyledons have fully expanded, remove both the 55% shade cloth and propagation domes.

8. Spray Plants With Finale Mixture. Wear gloves and protective clothing at all times.

        Prepare working Finale mixture by mixing 3 ml concentrated Finale in 48 oz of water in the Poly-TEK sprayer.
        Completely and evenly spray plants with a fine mist of the Finale mixture.
        Repeat Finale spraying every 3–4 days until only transformants remain. (Approximately 3 applications are necessary.)
        When satisfied that only transformants remain, discontinue Finale spraying.

9. Weed Out Excess Transformants.

Weed out excess transformants such that a maximum number of five plants per pot exist evenly spaced throughout the pot.

    
    


GFP Assay
Tissues are dissected by eye or under magnification using INOX 5 grade forceps and placed on a slide with water and coversliped. An attempt is made to record images of observed expression patterns at earliest and latest stages of development of tissues listed below. Specific tissues will be preceded with High (H), Medium (M), Low (L) designations.













Flower
pedicel receptacle nectary sepal petal filament anther pollen



carpel style papillae vascular epidermis stomata trichome


Silique
stigma style carpel septum placentae transmitting tissue



vascular epidermis stomata abscission zone ovule


Ovule
Pre-fertilization: inner integument outer integument embryo sac



funiculus chalaza micropyle gametophyte



Post-fertilization: zygote inner integument outer integument seed



coat primordia chalaza micropyle early endosperm mature



endosperm embryo


Embryo
suspensor preglobular globular heart torpedo late mature



provascular hypophysis radicle cotyledons hypocotyl


Stem
epidermis cortex vascular xylem phloem pith stomata trichome


Leaf
petiole mesophyll vascular epidermis trichome primordia



stomata stipule margin









T1 Mature: These are the T1 plants resulting from independent transformation events. These are screened between stage 6.50–6.90 (means the plant is flowering and that 50–90% of the flowers that the plant will make have developed) which is 4–6 weeks of age. At this stage the mature plant possesses flowers, siliques at all stages of development, and fully expanded leaves. We do not generally differentiate between 6.50 and 6.90 in the report but rather just indicate 6.50. The plants are initially imaged under UV with a Leica Confocal microscope. This allows examination of the plants on a global level. If expression is present, they are imaged using scanning laser confocal microscopy.
T2 Seedling: Progeny are collected from the T1 plants giving the same expression pattern and the progeny (T2) are sterilized and plated on agar-solidified medium containing M&S salts. In the event that there was no expression in the T1 plants, T2 seeds are planted from all lines. The seedlings are grown in Percival incubators under continuous light at 22° C. for 10–12 days. Cotyledons, roots, hypocotyls, petioles, leaves, and the shoot meristem region of individual seedlings were screened until two seedlings were observed to have the same pattern. Generally found the same expression pattern was found in the first two seedlings. However, up to 6 seedlings were screened before “no expression pattern” was recorded. All constructs are screened as T2 seedlings even if they did not have an expression pattern in the T1 generation.
T2 Mature: The T2 mature plants were screened in a similar manner to the T1 plants. The T2 seeds were planted in the greenhouse, exposed to selection and at least one plant screened to confirm the T1 expression pattern. In instances where there were any subtle changes in expression, multiple plants were examined and the changes noted in the tables.
T3 Seedling: This was done similar to the T2 seedlings except that only the plants for which we are trying to confirm the pattern are planted.
Image Data:
Images are collected by scanning laser confocal microscopy. Scanned images are taken as 2-D optical sections or 3-D images generated by stacking the 2-D optical sections collected in series. All scanned images are saved as TIFF files by imaging software, edited in Adobe Photoshop, and labeled in Powerpoint specifying organ and specific expressing tissues.
Instrumentation:
Microscope


    Inverted Leica DM IRB
    Fluorescence filter blocks:
    Blue excitation BP 450–490; long pass emission LP 515.
    Green excitation BP 515–560; long pass emission LP 590

Objectives

    HC PL FLUOTAR 5×/0.5
    HCPL APO 10×/0.4 IMM water/glycerol/oil
    HCPL APO 20×/0.7 IMM water/glycerol/oil
    HCXL APO 63×/1.2 IMM water/glycerol/oil

Leica TCS SP2 confocal scanner

    Spectral range of detector optics 400–850 nm.
    Variable computer controlled pinhole diameter.
    Optical zoom 1–32×.
    Four simultaneous detectors:
    Three channels for collection of fluorescence or reflected light.
    One channel for transmitted light detector.
    Laser sources:
    Blue Ar 458/5 mW, 476 nm/5 mW, 488 nm/20 mW, 514 nm/20 mW.
    Green HeNe 543 nm/1.2 mW
    Red HeNe 633 nm/10 mW


B. Far Red Induction (FRI) Procedure
Promoter lines were constructed in the two-component (HAP1-VP16) GFP reporter system. All promote lines were in the WS-2 background except PR0924, which was in Columbia (Col-0) ecotype. Seeds were plated on sterile 0.5% sucrose, 1× MS agar media and cold treated at 4° C. for 3–4 days before plates are put into growth chambers. Shade line induction conditions were as follows: All sets were placed on Conviron growth room shelf (16 hr L, 8 hr D cycling lights conditions (PAR=70 μE/m2s; R:FR=10.66) for 7 days. At 7 days, after planting, plates for far red induction (FRI) were placed under continuous far red LED light only, and exposed for 1 hr, 4 hr, and 24 hr. PR0924 lines were subjected to an additional 48 hr and 72 hr of FRI. White light (control) set remained under continuous white light for the same time period. All GFP expression analyses were preformed using the Typhoon imaging system. An exemplary map of the promoter construct PR0924 is shown in FIG. 1.
The results of the Shade Cloth Procedure are set forth in Table 1, which includes various information about each shade responsive promoter or promoter control element of the invention including the nucleotide sequence, the spatial expression promoted by each promoter, and the corresponding results from different expression experiments.







TABLE 1





Promoter Reports for Results of Shade Cloth Procedure
















Promoter Candidate ID: 15295937



 


Modulates the gene as identified by its GI number: 15235882


 


The GenBank description of the gene: homeobox-leucine zipper protein HAT4 (HD-Zip protein 4)


[Arabidopsis thaliana] >gi|462281|sp|Q05466|HAT4_ARATH Homeobox-leucine zipper protein


HAT4 (HD-ZIP protein 4) (HD-ZIP protein ATHB-2) >gi|629516|pir||S31424 DNA-binding homeotic


protein


 


The promoter sequence: (SEQ ID NO: 3)


caaccgtttttgtttagttcttctttaattaactttatcactaatgtttaaaagtaaaaaggtttttaaagtgtgcaacaagcgtgactctttggcctt


tagagtcatcaagaagggtaatcattttttttactctttctcgacaatagcaatcaaattatcattcccacttttaataatctcataaaataaagtcaa


tcatagttaaaatttgataaattccatggaaatgataaaaatttgattttactattgt


 


The Ceres cDNA ID of the endogenous coding sequence to the promoter:


 


cDNA nucleotide sequence: (nucleotides 1–255 of SEQ ID NO: 4)


ATCTTCTATCTCTCAAAAGAAAAGCAGACAACTTTATTTGCAAAAACAGAGTTTTTTTTTCTTATCTTGAGAAAGTTCAACAGAAGATGATGTTCGAGA


AAGACGATCTGGGTCTAAGCTTAGGCTTGAATTTTCCAAAGAAACAGATCAATCTCAAATCAAATCCATCTGTTTCTGTTACTCCTTCTTCTTCTTCTT


TTGGATTATTCAGAAGATCTTCATGGAACGAGAGTTTTACTTCTTCAGTTCCAAACT


 


Coding sequence: 13605987 (SEQ ID NO: 5)


MMFEKDDLGLSLGLNFPKKQINLKSNPSVSVTPSSSSFGLFRRSSWNESFTSSVPNSDSSQKETRTFIRGIDVNRPPSTAEYGDEDAGVSSPNSTVSSS


TGKRSEREEDTDPQGSRGISDDEDGDNSRKKLRLSKDQSAILEETFKDHSTLNPKQKQALAKQLGLRARQVEVWFQNRRARTKLKQTEVDCEFLRRCCE


NLTEENRRLQKEVTELRALKLSPQFYMHMSPPTTLTMCPSCEHVSVPPPQPQAATSAHHRSLPVNAWAPATRISHGLTFDALRPRS*


 


Promoter Candidate ID: 15295943


 


Modulates the gene as identified by its GI number: 15235927


 


The GenBank description of the gene: hypothetical protein [Arabidopsis thaliana] >gi|7486668|pir||


T04505 hypothetical protein F8F16.200 - Arabidopsis thaliana >gi|2827533|emb|CAA16541.1| hypo-


thetical protein [Arabidopsis thaliana] >gi|7270040|emb|CAB79856.1|


 


The promoter sequence: (SEQ ID NO: 6)


tgtttttcattttttttttcatttcgttactactaacagaacttttcatttatatcttgaaattttgttgtataactcaaataaagattgaaactaaca


tgatgatacttgtaattatctgattatttccttccatgtaaaccgatcaacatctagtcgtaaaacagaaaacaaaaaagacactgatcgacactcata


gcataacaaccgatcttagtatacatatgtgtgatatgttacgtcatatttagctcat


 


The Ceres cDNA ID of the endogenous coding sequence to the promoter: 13618832


 


cDNA nucleotide sequence: (SEQ ID NO: 7)


ATGTCTGGTGTGTGGGTATTCAACAAAAACGGAGTCATGAGGCTGGTGGAGAATCCTTACAACCAATCCGCCGGAGATTCGTCGGAATCGTCCTCTTCC


GGTGGTAACCAGCAGCAGAGGATGAGGAGGAAAATTCTCGTCCATCTTCCAAGCAGCGAGGTTGTGTCTTCGTACGGATCACTTGAGAAGATCTTGAAG


AATCTTGGGTGGGAGAGGTACTACAGTGGAGACAATACCGATCATCTGCTCCAGTTCCACAAGAGAACTTCGATCGATCTCATCTCTCTCCCTCGTGAC


TTCTCCAAGTTTAACTCTATTCACATGTATGATATCGTCGTCAAGAACCCTAACGTCTTCCATGTCCGTGACATGTAGTAGTCAATCATCCAAAACAAT


GGTTCAATATCATTCTCCGATCATCGCCGCTGGTGATATATCTATCATGTATATATATATGCAGGTTTTTATTTTGTCGTTGGGTGTTTTTGTTTTTGG


TTTATTTTGTTTTTAATGCATTTAATGTACGTGTTTTCCGTTCGACGTCGATCGATTGGGGTGGGTTCAAGCTAGAGCCATTCTAATAACTTTTATCAT


TTTGTGATTTTAATGAAATTGTATCATGTTG


 


Coding sequence: (SEQ ID NO: 8)


MSGVWVFNKNGVMRLVENPYNQSAGDSSESSSSGGNQQQRMRRKILVHLPSSEVVSSYGSLEKILKNLGWERYYSGDNTDHLLQFHKRTSIDLISLPRD


FSKFNSIHMYDIVVKNPNVFHVRDM*


 


Promoter Candidate ID: 15295955


 


Modulates the gene as identified by its GI number: 15226394


 


The GenBank description of the gene: hypothetical protein; protein id: At2g28400.1, supported by


cDNA: gi_17979316 [Arabidopsis thaliana] >gi|25350263|pir||D84684 hypothetical protein At2g28400


[imported] - Arabidopsis thaliana thaliana]


 


The promoter sequence: (SEQ ID NO: 9)


tcaataacaatttaacaaataccaagataatatataaagttaattaaagttttcagttctgcttatttttgagcaaatatagtgataataagacatttt


actttttaaaactcggaaaggatgcgttgtttttattaaaccttaaagtggtatttaaaatttcaaatattttttaaaatttataaacgaaattcaagt


tttgagcaaatttgtttttaatatacgatagaatgataaataagtataaactgaagt


 


The Ceres cDNA ID of the endogenous coding sequence to the promoter: 4905232


 


cDNA nucleotide sequence: (SEQ ID NO: 10)


cttaaaaccaaaaacaaagtttcatttcttcttcttcttgaaatggcgacgagcaagtgctactatccacggccaagccaccgtttcttcaccactgac


caacacgtcaccgccacttccgatttcgagctagacgaatgggatcttttcaataccggttcagattcctcttcaagtttcagctttagtgaccttaca


atcacatccggtcgaaccggaactaaccggcaaattcacggtggttctgactccggtaaagctgcgtcttctctaccggttaacgtaccggactggtct


aagattcttggagacgagagtcgacgacagaggaagatttcgaatgaggaagaagttgacggagatgaaattttatgcggcgaaggtacacggcgagtt


ccaccgcatgaattgcttgcgaaccggaggatggcttcgttttcggttcatgaaggtgctgggaggactttgaaaggaagagatctgagtagggtgcga


aatactatttttaaaa


 


Coding sequence: (SEQ ID NO: 11)


MATSKCYYPRPSHRFFTTDQHVTATSDFELDEWDLFNTGSDSSSSFSFSDLTITSGRTGTNRQIHGGSDSGKAASSLPVNVPDWSKILGDESRRQRKIS


NEEEVDGDEILCGEGTRRVPPHELLANRRMASFSVHEGAGRTLKGRDLSRVRNTIFK


 


Promoter Candidate ID: 15295958


 


Modulates the gene as identified by its GI number: 11357157


 


The GenBank description of the gene: acyl CoA reductase-protein - Arabidopsis thaliana >gi|7635476|


emb|CAB88536.1| acyl CoA reductase-protein [Arabidopsis thaliana]


 


The promoter sequence: (SEQ ID NO: 12)


aagatagtacagtttcagtgttttgagaaaaaaagctgaactaaaactaaaatgtttaaggacacaatatttagtttcaattagataattcaacagttt


gaacaattttttttttttttttttgaagtcatttatttatacaatgttttaaaacgcattaagcatttaggcagccgacaaacgcctattgtctaactg


taaataggcgcttccacttaggttcatattgcatatttactatatgtgtatagtgac


 


The Ceres cDNA ID of the endogenous coding sequence to the promoter: 13611606


 


cDNA nucleotide sequence: (nucleotides 1–255 of SEQ ID NO: 13)


ACGTGACTCAATAAAATCAAGTCTTTTGTTTCCTTTTATCCAAAAAAAAAAAAAAGTCTTGTGTTTCTCTTAGGTTGGTTGAGAATCATTTCATTTCAA


TGGAATCCAATTGTGTTCAATTTCTCGGTAACAAGACCATTCTCATCACAGGAGCTCCTGGTTTTCTTGCCAAGGTTTTGGTAGAGAAAATACTAAGGT


TGCAACCAAATGTGAAGAAGATATACCTTCTGTTGAGAGCTCCCGACGAAAAATCAG


 


Coding sequence: (SEQ ID NO: 14)


MESNCVQFLGNKTILITGAPGFLAKVLVEKILRLQPNVKKIYLLLRAPDEKSAMQRLRSEVMEIDLFKVLRNNLGEDNLNALMREKIVPVPGDISIDNL


GLKDTDLIQRMWSEIDIIINIAATTNFDERYDIGLGINTFGALNVLNFAKKCVKGQLLLHVSTAYISGEQPGLLLEKPFKMGETLSGDRELDINIEHDL


MKQKLKELQDCSDEEISQTMKDFGMARAKLHGWPNTYVFTKAMGEMLMGKYRENLPLVIIRPTMITSTIAEPFPGWIEGLKTLDSVIVAYGKGRLKCFL


ADSNSVFDLIPADMVVNAMVAAATAHSGDTGIQAIYHVGSSCKNPVTFGQLHDFTARYFAKRPLIGRNGSPIIVVKGTILSTMAQFSLYMTLRYKLPLQ


ILRLINIVYPWSHGDNYSDLSRKIKLAMRLVELYQPYLLFKGIFDDLNTERLRMKRKENIKELDGSFEFDPKSIDWDNYITNTHIPGLITHVLKQ*


 


Promoter Candidate ID: 15295970


 


Modulates the gene as identified by its GI number: 15230001


 


The GenBank description of the gene: hypothetical protein; protein id: At3g29575.1, supported by


cDNA: gi_14326573 [Arabidopsis thaliana] >gi|14326574|gb|AAK60331.1|AF385741_1 AT3g29575/MWE13_2


[Arabidopsis thaliana] >gi|22137322|gb|AAM91506.1|


 


The promoter sequence: (SEQ ID NO: 15)


acggtcaaagtattgctaacatggtcattacattgaaaaagaaaattaattgtctttactcatgtttattctatacaaataaaaatattaaccaaccat


cgcactaacaaaatagaaatcttattctaatcacttaattgttgacaattaaatcattgaaaaatacacttaaatgtcaaatattcgttttgcatactt


ttcaatttaaatacatttaaagttcgacaagttgcgtttactatcatagaaaactaa


 


The Ceres cDNA ID of the endogenous coding sequence to the promoter: 12736859


 


cDNA nucleotide sequence: (nucleotides 1–255 of SEQ ID NO: 16)


AAATTCTCTTTGGGCTCTTAATTTCTTTTTGAGTGTTCGTTCGAGATTTGTCGGAGATTTTTTCGGTAAATGTTGAAATTTTGTGGGATTTTTTTTTAT


TTCTTTATTAAACTTTTTTTTATTAATTTATAAAAAGGGAAGGTCGTCATTAATCGAAGAAATGGAATCTTCCAAAATTTGATATTTTGCTGTTTTCTT


GGGATTTGAATTGCTCTTTATCATCAAGAATCTGTTAAAATTTCTAATCTAAAATC


 


Coding sequence: (SEQ ID NO: 17)


MSKKQRLSEEDGEVEIELDLGLSLNGRFGVDPLAKTRLMRSTSVLDLVVNDRSGLSRTCSLPVETEEEWRKRKELQSLRRLEAKRKRSEKQRKHKACGG


EEKVVEEGSIGSSGSGSSGLSEVDTLLPPVQATTNKSVETSPSSAQSQPENLGKEASQNIIEDMPFVSTTGDGPNGKKINGFLYRYRKGEEVRIVCVCH


GSFLSPAEFVKHAGGGDVAHPLKHIVVNPSPFL*


 


Promoter Candidate ID: 15295973


 


Modulates the gene as identified by its GI number: 15233496


 


The GenBank description of the gene: auxin-responsive protein IAA1 (Indoleacetic acid-induced


protein 1) [Arabidopsis thaliana] >gi|12644289|sp|P49677|AXI1_ARATH Auxin-responsive protein


IAA1 (Indoleacetic acid-induced protein 1)


 


The promoter sequence: (nucleotides 1–255 of SEQ ID NO: 74)


aaaatgttatttgagacagcatatcacatggccttaccatacttcctgcatccattattccattaagaacactcttcaccctcatccacatgcatctcc


ctccccaatttatttactattgatcataattgtacaaacctatacttacaatttatatatgtgtctacgagaaaataaataatattttacagtgttttg


tctattattttgttctatagtttcttgcaaacaaaacattacttttcacgcaaaaac


 


The Ceres cDNA ID of the endogenous coding sequence to the promoter: 13617391


 


cDNA nucleotide sequence: (SEQ ID NO: 80)


ACACAAGCATTTTCAAGGATATCAAATCACAATCCCAAGAAGAGCAATAACAAGAGAAGAAGAAGTAGTTCAAGAATTAAGGAAGAGAGCTTCTCCGTT


AAAGTATAGTGAGAGAATATGGAAGTCACCAATGGGCTTAACCTTAAGGACACAGAGCTTCGTTTGGGATTACCCGGAGCACAGAAGAACAACAACTAG


AACTTTCTTGCGTCAGAGCAACAACAAGCGCAAGAACAACGACTCAACAGAAGAATCTGCTCCTCCTCCTGCAAAAACACAAATCGTTGGATGGCCTCC


AGTGAGATCTAACCGTAAGAACAACAACAACAAAAACGTGAGTTATGTGAAAGTGAGTATGGACGGAGCTCCATATCTCCGTAAGATAGATCTCAAGAT


GTACAAAAACTATCCAGAGCTTCTCAAAGCACTAGAGAACATGTTCAAGTTCACAGTAGGTGAATATTCCGAGAGAGAAGGCTACAAAGGATCTGGATT


TGTACCTACTTATGAAGACAAAGATGGAGATTGGATGTTGGTCGGTGATGTTCCATGGGACATGTTCTCTTCATCTTGTCAAAAACTCAGAATCATGAA


AGGATCCGAAGCTCCTACTGCCTTATGATCCATTGTCTCAAAACACCTTTTGGTCGAGGCAAAAACAAATTCTACTTTGTTTAGATAAAAAAAAGTTTG


GTGTAAGAAAGAAAAAGCAATAGGGTTACAAATACGTTATATAGATGTAAACTAGCTTTGGTTAATTCTGTAAAAGATGAGTTTTGATTATACGAAGTT


TATATGT


 


Coding sequence: (SEQ ID NO: 81)


MEVTNGLNLKDTELRLGLPGAQEEQQLELSCVRSNNKRKNNDSTEESAPPPAKTQIVGWPPVRSNRKNNNNKNVSYVKVSMDGAPYLRKIDLKMYKNYP


ELLKALENMFKFTVGEYSEREGYKGSGFVPTYEDKDGDWMLVGDVPWDMFSSSCQKLRIMKGSEAPTAL*


 


Promoter Candidate ID: 15295976


 


Modulates the gene as identified by its GI number: 15238721


 


The GenBank description of the gene: auxin-induced protein-like; protein id: At5g18060.1


[Arabidopsis thaliana] >gi|9757898|dbj|BAB08405.1| auxin-induced protein-like [Arabidopsis


thaliana]


 


The promoter sequence: (SEQ ID NO: 18)


gtgggacaaactagagcaagagttcacatggttctgtctctaccatttggaaaagatgcattaatgtaacttgtcttggtgagataattaacaaactcc


atatgcaattcacaagggcttgtttgctcaatgttttgtttagataagacatattctactgtcaataataaaggccagcaactttctcttcttcaaatt


ctgtgatgatctattcttgaatctctgtggtctaaaattgtaaatggggtttaataagaaattatagtgggtactgatgttgttcaacaacagaacaac


aaatcctatcgtttaaaacattgaaaaaacagtcctttgtgaacttatggagtttgtttttcgtttactgtcccacactcaatttattgttagattatc


tcatcaagacgaactgcattaaactaaatctttccagatggtaaagacatattgataggcaacataatcttagctcgccgtgagaatccatcttttgca


tatctgcttcaacaatggtttgctcatgagtaatctctgcattctcataatctcatttcatgattaggcttttaaaaaaaatcttagctatgccaagct


cttgctaagaaaatgttcctcttggtaatgataatcacagtttatccaaaaaaaaacaaaaaacagaaccatgtgaactctgtcccacgcttcaccaag


caatccattaacttgaatctttcatacatcttttcagaagctttaaaaataattcaaactttcagacaaaagaa


 


The Ceres cDNA ID of the endogenous coding sequence to the promoter: 4945558


 


cDNA nucleotide sequence: (SEQ ID NO: 19)


atcaaccaacaccaagcaatccattaacttgaatctttcatacatcttttcagaagctttaaaaataattcaaactttcagacaaaagaaatggctttg


gtgagaagtctattggttgcaaagaagattcttagccgctccgccgcagcagtctcggcgccaccaaaagggtttcttgcagtgtacgtaggagagagc


cagaagaagagatatttagtgccactctcatacttgaaccagccttcttttcaagctctgctcagtaaatccgaagaagagtttgggttcgatcatccg


atgggtggcttaacgatcccttgtcccgaagatactttcatcaatgtgacttctcggctccattgatgattatccaacatagtgttttttcgagttaga


gatagagttgtttccttgtaaatagaggaattttttgttccttttttttttttttttttctctttcatcttgaaaaagttcttctaaattttttggaag


tggatgtagatgcagtttttgtgctatatacacaatcataattcatgttaacacattttggatcgattatggaaaaagaatggatat


cacc


 


Coding sequence: (SEQ ID NO: 20)


MALVRSLLVAKKILSRSAAAVSAPPKGFLAVYVGESQKKRYLVPLSYLNQPSFQALLSKSEEEFGFDHPMGGLTIPCPEDTFINVTSRLH*


 


Promoter Candidate ID: 15295997


 


Modulates the gene as identified by its GI number: 18406162


 


The GenBank description of the gene: expressed protein [Arabidopsis thaliana] >gi|21592337|gb|


AAM64288.1| unknown [Arabidopsis thaliana] >gi|26451672|dbj|BAC42932.1| unknown protein


[Arabidopsis thaliana] >gi|28973149|gb|AAO63899.1| unknown protein


[Arabidopsis thaliana]


 


The promoter sequence: (SEQ ID NO: 82)


tagctagatttctatataaacagaagaaagttaaaaagcaaataaaaattcacaaatagaaatcgaacaaaaagctatgaaaatataaataccataacc


ttatggaaaaacgatgaaatgcttaacaaaaaaaactttggcaatggcatgcatgtgcctgtaacagaaggcccccataagctgttagtgatatacaac


ttaagcaaatgtgcactcttcacgcacttcccgcttttctaaatttcaatttatttg


 


The Ceres cDNA ID of the endogenous coding sequence to the promoter: 13486695


 


cDNA nucleotide sequence: (SEQ ID NO: 22)


GCCATCTTCTTCATTATCATCATCTCCATCTCTCTCTCTCTCTCTCTCATTTTCTTGAAAAAGATGAGAACCTTAAAGACTCAGACCACAAGGGGAAGA


AGAAGAGCAAATGTGTCGTCACGTACGAGAGTTTTACACACGTGCTGTGGAAATGGTAGTAGCGACGGAGGGAAGACGGTGATGGAGAAGCTTCTTGCG


TTAAAGAGCCTTCTTCCTCCACCGGTGAATGTCGGTGGTGGAGAGACGGAGGAGCTGTTTCAAGAGACGGCGGAGTATATCGTGAAGCTTAGAACACAA


GTCGTGGTGTTGAAGAAACTGATTGAGATTTACGATAACTCTTCTGATCAGAAGAAAGATGTTGTTTTATAATGTTCATTTATATTTTCTTTAATTTAA


ATTATTTCAGGTTTTTCTGTTTTTTTTTGTTATAAACTTATAATTATTATATTGTGATCCGTAATGGTTTTAGGTTGTCCATGTCTTTAATGTATTGGT


TTAAAGGAAAAAGTATTGATGATTG


 


Coding sequence: (SEQ ID NO: 23)


MRTLKTQTTRGRRRANVSSRTRVLHTCCGNGSSDGGKTVMEKLLALKSLLPPPVNVGGGETEELFQETAEYIVKLRTQVVVLKKLIEIYDNSSDQ


KKDVVL*


 


Promoter Candidate ID: 15295940


 


Modulates the gene as identified by its GI number: 18417976


 


The GenBank description of the gene: Expressed protein; protein id: At4g32280.1, supported by cDNA:


gi_14190492 [Arabidopsis thaliana]


 


The promoter sequence: (nucleotides 1–255 of SEQ ID NO: 58)


cagccgtaaatccttccataaatttattttgcaagttttgctcattatataatgagcggaatttatgatataatcgtttgtaataatgttatgttttg


atcaaaatttgaaattaaaagtaggtgagaacttgttatacagtgtagataaggtggatcttgaatataaaaataaaatttataagatgtatttaaag


cagaaaagcataaaactttagataaaataatgtaaaaatgtgttagcatcaatgttggg


 


The Ceres cDNA ID of the endogenous coding sequence to the promoter: 12655184


 


cDNA nucleotide sequence: (SEQ ID NO: 83)


AATCAACACCAACGAACACAACCTTTTCCAAAGCCAATAATAAAAGAACAAAAGCTTTTAGTTTCATCAAAGACGAAGCTGCCTTAGAAATGGAGTTGG


ATCTTGGTCTATCTCTTTCACCTCATAAATCTTCCAAGTTAGGGTTTAACTTTGACCTCAACAAGCATTGTGCGATCGAGGGTGCTGCGTCTTGTTTGG


GTACCGAAAAACTGCGTTTTGAGGCGACGTTTGGGTTAGGGAATGTGGAGGAAAATT


 


Coding sequence: (SEQ ID NO: 26)


MELDLGLSLSPHKSSKLGFNFDLNKHCAIEGAASCLGTEKLRFEATFGLGNVEENCYMPKQRLFALNGQPNEEDEDPLESESSIVYDDEEENSEVVGWP


PVKTCMIKYGSYHHRHIRHIRNHHHCPYHHRGRRITAMNNNISNPTTATVGSSSSSSISSRSSMYVKVKMDGVAIARKVDIKLFNSYESLTNSLITMFT


EYEDCDREDTNYTFTFQGKEGDWLLRGDVTWKIFAESVHRISIIRDRPCAYTRCLF*


 


Promoter Candidate ID: 15295946


 


Modulates the gene as identified by its GI number: 18378953


 


The GenBank description of the gene: bHLH protein (HFR1) [Arabidopsis thaliana] >gi|20532238|sp|


Q9FE22|HFR1_ARATH Long hypocotyl in far-red 1 (bHLH-like protein HFR1) (Reduced phytochrome


signaling) (Basic helix-loop-helix FBI1 protein) (Reduced sensitivity to far-red


 


The promoter sequence: (SEQ ID NO: 21)


aatttatctctatgttcatgtgtcaaagtggtagtgaatctagtgacgttattgattaatcaagattacttttatctttctgtgcaaaatttcaagat


tactctaaagtcgatatatgctactatgacgtagttttgggacaattacgtatagaatcataaaaacaataagcagaataataatccatttaagtaca


ttgtgaatttgtgataatggaattatttgacaatacttttccaaaataaaaactaatttaattactgtattaattattttagtaaaacaatattttca


ttacaatgtttgttgtgaatccaaaaaagtattgtttccaaagaactcaaatgacatcaatatgtctataataacctcgtgtagctgtatgttagaat


ctagccgaattgttttattgttgtcggtgtacgcaacaaacgaaccacacatactttgaaacgtggcacaatataagtgggtcaccaatgtagctgac


aactataccatctatctgatccgatcgctcttataacataagcgtatgggataccattttctcggacaaagctgaaatccctaaagaaaaaacacttc


tccaaacttttcatctccgatatctctttaactaac


 


The Ceres cDNA ID of the endogenous coding sequence to the promoter: 13488199


 


cDNA nucleotide sequence: (SEQ ID NO: 84)


TAAGTGGGTCACCAATGTAGCTGACAACTATACCATCTATCTGATCCGATCGCTCTTATAACATAAGCGTATGGGATACCATTTTCTCGGACAAAGCTG


AAATCCCTAAAGAAAAAACACTTCTCCAAACTTTTCATCTCCGATATCTCTTTAACTAACATGTCGAATAATCAAGCTTTCATGGAATTGGGATGGAGA


AACGACGTCGGATCACTTGCTGTGAAAGATCAGGGCATGATGTCAGAAAGAGCAAGA


 


Coding sequence: (SEQ ID NO: 85)


MSNNQAFMELGWRNDVGSLAVKDQGMMSERARSDEDRLINGLKWGYGYFDHDQTDNYLQIVPEIHKEVENAKEDLLVVVPDEHSETDDHHHIKDFSERS


DHRFYLRNKHENPKKRRIQVLSSDDESEEFTREVPSVTRKGSKRRRRDEKMSNKMRKLQQLVPNCHKTDKVSVLDKTIEYMKNLQLQLQMMSTVGVNPY


FLPATLGFGMHNHMLTAMASAHGLNPANHMMPSPLIPALNWPLPPFTNISFPHSSSQSLFLTTSSPASSPQSLHGLVPYFPSFLDFSSHAMRRL*


 


Promoter Candidate ID: 15295949


 


Modulates the gene as identified by its GI number: 18415376


 


The GenBank description of the gene: sulfotransferase family [Arabidopsis thaliana] >gi|20466686|


gb|AAM20660.1| steroid sulfotransferase-like protein [Arabidopsis thaliana] >gi|21537216|gb|


AAM61557.1| steroid sulfotransferase-like protein [Arabidopsis thaliana]


 


The promoter sequence: (SEQ ID NO: 24)


aaaaccgttagtttgtaaaaccaagccggaaagagaaaacttatattattaatcatatgcaaatatttattaaaatagttataatataatataatca


aatatataatttttcaaagttctttttacacagaaccaaactgaaattgcgtcaaacctaagcaaaaacctaacctgaatcactactagttgagatt


gcattaaaaaaaattgataaagaaaacaaaatcagtcaattttctatttattttactaggg


 


The Ceres cDNA ID of the endogenous coding sequence to the promoter: 13492429


 


cDNA nucleotide sequence: (nucleotides 1–255 of SEQ ID NO: 25)


ACACCAACACACAAAGATTCCATTACAAATAAACAATTTTCATATATATCTATAACAAAAAAAAACAATGGCTACCTCAAGCATGAAGAGCATTCCAAT


GGCGATCCCAAGTTTCTCCATGTGTCACAAGCTCGAGCTCCTTAAAGAAGGCAAAACTCGCGACGTCCCGAAAGCCGAAGAAGATGAAGGGCTAAGCTG


CGAGTTCCAAGAGATGTTGGATTCTCTTCCTAAGGAGAGAGGATGGAGAACTCGTTA


 


Coding sequence: (SEQ ID NO: 29)


MATSSMKSIPMAIPSFSMCHKLELLKEGKTRDVPKAEEDEGLSCEFQEMLDSLPKERGWRTRYLYLFQGFWCQAKEIQAIMSFQKHFQSLENDVVLATI


PKSGTTWLKALTFTILNRHRFDPVASSTNHPLFTSNPHDLVPFFEYKLYANGDVPDLSGLASPRTFATHLPFGSLKETIEKPGVKVVYLCRNPFDTFIS


SWHYTNNIKSESVSPVLLDQAFDLYCRGVIGFGPFWEHMLGYWRESLKRPEKVFFLRYEDLKDDIETNLKRLATFLELPFTEEEERKGVVKAIAELCSF


ENLKKLEVNKSNKSIKNFENRFLFRKGEVSDWVNYLSPSQVERLSALVDDKLGGSGLTFRLS*


 


Promoter Candidate ID: 15295952


 


Modulates the gene as identified by its GI number: 15241451


 


The GenBank description of the gene: putative protein; protein id: At5g44260.1, supported by cDNA:


gi_14334449 [Arabidopsis thaliana] >gi|10176881|dbj|BAB10111.1|gb|AAD10689.1~gene_id:K9L2.1~


similar to unknown protein [Arabidopsis thaliana]


 


The promoter sequence: (nucleotides 1–255 of SEQ ID NO: 70)


ttgtttaacacctcaaacctgttaagactaatcacaatgttcgaagataatgccatttctatatatatttagtatagcatcacacatgcgttctgtgtt


gcaaagtttactctagagttatcactgagtcatgactcatgatgaccattattatagtattagtacttttaagttttaggtcgagaatatgaagctaat


acatgcatgtaatgatgtaaatatgcctaccttaaaaaatatcgaattattcagaaa


 


The Ceres cDNA ID of the endogenous coding sequence to the promoter: 12601699


 


cDNA nucleotide sequence: (SEQ ID NO: 86)


ATCCCACACTTATCTCTTCCTATCTCTCTCTCATTCAAACCCAAATAGGAAACAAATACACAAAAGTATAATAAAAAGTCTTTCTCTCATCTTTCGCCA


CGTAGACATGGACGTCGAACATCACAAATCCGGCCACATCAGTAGACCAACGGTGGATATTCCACCGAGGAAGCTTCTTTCCTCCGCCAAGTCTCCGTC


GTCAGTTTCAAGTCCCCTTCGCGACTATAAAGAACAGAAAGACTATTGTTACGACTC


 


Coding sequence: (SEQ ID NO: 87)


SHTYLFLSLSHSNPNRKQIHKSIIKSLSLIFRHVDMDVEHHKSGHISRPTVDIPPRKLLSSAKSPSSVSSPLRDYKEQKDYCYDSDSEDPYAGDHFRMY


EFKIRRCTRSRSHDWTDCPFSHPGEKARRRDPRRFHYTGEVCPEFSRHGDCSRGDECGFAHGVFECWLHPSRYRTEACKDGKHCKRKVCFFAHSPRQLR


VLPPSPENHISGGCGGSPSSSPASVLSNKNNRCCLFCSHSPTSTLLNLSRSPSSSPPLSPADKADAFSRLSRRRTAVLNELISSLDSLSLTEALAASSS


SPVTMPISTATMIASSNLSSNHHHHRLPPWLDVGDRDLQLQQSSPLRFALSPSSTPSYLHGQLQPPPSSFFGDEFTPRGGRLSDFSVAAAAAAQARDKN


SFEVGSSGDLDLGWVNDLLT*


 


Promoter Candidate ID: 15295961


 


Modulates the gene as identified by its GI number: 15218709


 


The GenBank description of the gene: flowering signals mediating protein FT; protein id:


At1g65480.1, supported by cDNA: gi_17529185 [Arabidopsis thaliana] >gi|17432933|sp|Q9SXZ2|FT_ARATH


FLOWERING LOCUS T protein >gi|25346243|pir||T52447 FT protein [validated] - Arabidopsis


 


The promoter sequence: (SEQ ID NO: 27)


ataatatggccgcttgtttataaaaaaagaagagaaataaaacaattgatttggtttatattatttaattgcagatatcttgtacttaattcattttga


gataattttgcgtatttgagttcggacattggtaggtatggacgatgaaaataactgccttcattctacatgtttgagatttgtttgtcgaccatataa


cacaagcggctagaaaaataggtgactattctcaaatgtcctggttctatctaacct


 


The Ceres cDNA ID of the endogenous coding sequence to the promoter: 12581196


 


cDNA nucleotide sequence: (SEQ ID NO: 28)


ACAATTAAAGAAGCAGAAACAAAAACAAGTAAAACAGAAACAATCAACACAGAGAAACCACCTGTTTGTTCAAGATCAAAGATGTCTATAAATATAAGA


GACCCTCTTATAGTAAGCAGAGTTGTTGGAGACGTTCTTGATCCGTTTAATAGATCAATCACTCTAAAGGTTACTTATGGCCAAAGAGAGGTGACTAAT


GGCTTGGATCTAAGGCCTTCTCAGGTTCAAAACAAGCCAAGAGTTGAGATTGGTGGAGAAGACCTCAGGAACTTCTATACTTTGGTTATGGTGGATCCA


GATGTTCCAAGTCCTAGCAACCCTCACCTCCGAGAATATCTCCATTGGTTGGTGACTGATATCCCTGCTACAACTGGAACAACCTTTGGCAATGAGATT


GTGTGTTACGAAAATCCAAGTCCCACTGCAGGAATTCATCGTGTCGTGTTTATATTGTTTCGACAGCTTGGCAGGCAAACAGTGTATGCACCAGGGTGG


CGCCAGAACTTCAACACTCGCGAGTTTGCTGAGATCTACAATCTCGGCCTTCCCGTGGCCGCAGTTTTCTACAATTGTCAGAGGGAGAGTGGCTGCGGA


GGAAGAAGACTTTAGATGGCTTCTTCCTTTATAACCAATTGATATTGCATACTCTGATGAGATTTATGCATCTATAGTATTTTAATTTAATAACCATTT


TATGATACGAGTAACGAACGGTGATGATGCCTATAGTAGTTCAATATATAAGTGTGTAATAAAAATGAGAGGGGGAGGAAAATGAGAGTGTTTTACTTA


TATAGTGTGTGATGCGATAATTATATTAATCTACATGAAATGAAGTGTTATATTTATACTTT


 


Coding sequence: (SEQ ID NO: 88)


MSINIRDPLIVSRVVGDVLDPFNRSITLKVTYGQREVTNGLDLRPSQVQNKPRVEIGGEDLRNFYTLVMVDPDVPSPSNPHLREYLHWLVTDIPATTGT


TFGNEIVCYENPSPTAGIHRVVFILFRQLGRQTVYAFGWRQNFNTREFAEIYNLGLPVAAVFYNCQRESGCGGRRL*


 


Promoter Candidate ID: 15295964


 


Modulates the gene as identified by its GI number: 21554820


 


The GenBank description of the gene: putativepod-specific dehydrogenase SAC25 [Arabidopsis thaliana]


 


The promoter sequence: (nucleotides 24–279 of SEQ ID NO: 66)


aattaaatgaaactcgcccctaaattaggagggatttgggtaagtggtaacacattcactggaaacatgtgaagaaaggaggatgtcaagtagctgaaa


actcagtatagtaaccaacggcttctcaccaacctttcattaataatttggtcatccctatatttttattcaacattttgtttttcaatagcttagagc


accttaatacctttcagtgtttttttataaaaaaaaacaaaaattgggattaatcat


 


The Ceres cDNA ID of the endogenous coding sequence to the promoter: 12712683


 


cDNA nucleotide sequence: (SEQ ID NO: 89)


CTCCCAAACCTATCTTCTTCTTCCTCTCTTGTCTCTCTCGCTCTCTCTCTTCTACATTGTTTCTTGAGGTCAATCTATTAAAAATGGGATTATATTCAC


TAATCACAGGAAGAAGAGGACCAAGTGGATTTGGTTCAGCTTCAACAGCTGAAGAGGTTACTCAAGGGATTGATGCAACTAATCTCACTGCAATTATCA


CAGGAGGGACAGGAGGAATAGGGATGGAGACAGCGAGAGTGCTGTCGAAGAGAGGTG


 


Coding sequence: (SEQ ID NO: 90)


MGLYSLITGRRGPSGFGSASTAEEVTQGIDATNLTAIITGGTGGIGMETARVLSKRGAHVVIGARNMGAAENAKTEILRQNANARVTLLQLDLSSIKSI


KAFVREFHALHLPLNLLINNAGVMFCPYQLSEDGIELQFATNHIGHFLLTNLLLDTMKNTAKTSGVEGRILNVSSVAHIYTVQEGIQFDSINDICSYSD


KRAYGQSKLANILHANELSRQLQEEGVNITANSVHPGLILTNLFQHTALLMRFLKFFSFYLWKNIPQGAATTCYVALHPSVKGVTGKYFADCNEVTPSK


LARDETLAQKLWDFSVKLINSVSKKNYLGFDDTT*


 


Promoter Candidate ID: 15295967


 


Modulates the gene as identified by its GI number: 15241765


 


The GenBank description of the gene: putative protein; protein id: At5g62280.1 [Arabidopsis thaliana]


>gi|8809641|dbj|BAA97192.1|gb|AAE82627.1~gene_id:MMI9.11~similar to unknown protein [Arabidopsis


thaliana]


 


The promoter sequence: (SEQ ID NO: 30)


taagaaaaactgtnggcttgttgtcagaacaaacatggacccatgttctctatgtccctaagatgtgtaccaatctcaattcacttcttttgttgcact


attttttaaaaaataacttttattttatattttgagatctccattgcccctgctgcactagacattacagctcattttttccttataattcaatcccta


gctatttttctttcttattagtttaaactaatcatatttgggtaattagcgttgaaa


 


The Ceres eDNA ID of the endogenous coding sequence to the promoter: 12732583


 


cDNA nucleotide sequence: (SEQ ID NO: 31)


ATGGCTTTTTGGTCTGCTGAGAATGCTACTAAAGCCTATCTTAGTACATTGAAAACGGATCAAAGGACAAAAGAACCAAACGTCGCCGAATTCATATCA


GCCCTAGCCGCCGGAAATAGCGCTAGAAAGATAGCCGTGGCTTGCGCCGGAGCAGCAAACGCCGACATACTCGTTGCACTAATCGCAGCGGCTAACCAA


ACGCGTGGTCAAGTTGTATGCGTTTTACGTGGTATCGAAGAACTAATCATATCCCAAAAAATGTTGGAACCATCAGAGATTCATCAGATACAATTCGTA


GTCGGAGAATCTAACGACGACACTCTAATCAATAATCATTTCGGAGAAGCAGATTTCGTCCTCGTGGATTGTAACCTCGAAAACCACCAAGAGATCGTT


GGAAAAATCCTTAATCATCACGAAGAAAACGCAAGAACCGGGGGTGGAAGCGGTGTGGCGGTTGTGGTGGGTTATAACGCGTTTTCGAGAGGGTCATGG


AGGTTTAGCGATGGAAGGAAAACGCAGTTTTTACCTATAGGAGAAGGGTTACTTGTGACGAGGGTCAATGATAATCAGAAGATGATGATGAAAAATCAC


CATCGTGACCAAGTGATGAGGAAGAGTCGTTGGGTGGTGAAGGTTGATAAGTGCACTGGAGAGGAACATGTGTTTAGGGTTAGGGTTCCCCGAGGAGAA


GCCATTATTGAAGCTTAA


 


Coding sequence: (SEQ ID NO: 32)


MAFWSAENATKAYLSTLKTDQRTKEPNVAEFISALAAGNSARKIAVACAGAANADILVALIAAANQTRGQVVCVLRGIEELIISQKMLEPSEIHQIQFV


VGESNDDTLINNHFGEADFVLVDCNLENHQEIVGKILNHHEENARTGGGSGVAVVVGYNAFSRGSWRFSDGRKTQFLPIGEGLLVTRVNDNQKMMMKNH


HRDQVMRKSRWVVKVDKCTGEEHVFRVRVPRGEAIIEA*


 


Promoter Candidate ID: 15295985


 


Modulates the gene as identified by its GI number: 34910002


 


The GenBank description of the gene: putative cytokinin oxidase [Oryza sativa (japonica cultivar-


group)] >gi|22202687|dbj|BAC07345.1| putative cytokinin oxidase [Oryza sativa (japonica cultivar-


group)]


 


The promoter sequence: (nucleotides 1–255 of SEQ ID NO: 76)


cactacacacgtgtgacctcatcctctcccacgtgaatatccacgtggcgttcttccgttccgtttctcccatccctcccatgcctctccccatgactc


tatttatcccaatcctctcttcctttcattaatttatcagttaaaattcctcttttttcctagtagtatttggagttttcatatcaaaaagtttagact


aaccctaaaaacattgatagaaaaacttatcattttaaacgttcttggggaccaatc


 


The Ceres cDNA ID of the endogenous coding sequence to the promoter: 12721545


 


cDNA nucleotide sequence: (SEQ ID NO: 91)


ATGAATCGTGAAATGACGTCAAGCTTTCTTCTCCTGACGTTCGCCATATGTAAACTGATCATAGCCGTGGGTCTAAACGTGGGCCCCAGTGAGCTCCTC


CGCATCGGAGCCATAGATGTCGACGGCCACTTCACCGTCCACCCTTCCGACTTAGCCTCCGTCTCCTCAGACTTCGGTATGCTGAAGTCACCTGAAGAG


CCATTGGCCGTGCTTCATCCATCATCGGCCGAAGACGTGGCACGACTCGTCAGAACA


 


Coding sequence: (SEQ ID NO: 92)


MNREMTSSFLLLTFAICKLIIAVGLNVGPSELLRIGAIDVDGHFTVHPSDLASVSSDFGMLKSPEEPLAVLHPSSAEDVARLVRTAYGSATAFPVSARG


HGHSINGQAAAGRNGVVVEMNHGVTGTPKPLVRPDEMYVDVWGGELWVDVLKKTLEHGLAPKSWTDYLYLTVGGTLSNAGISGQAFHHGPQISNVLELD


VVTGKGEVMRCSEEENTRLFHGVLGGLGQFGIITRARISLEPAPQRVRWIRVLYSSFKVFTEDQEYLISMHGQLKFDYVEGFVIVDEGLVNNWRSSFFS


PRNPVKISSVSSNGSVLYCLEITKNYHDSDSEIVDQEVEILMKKLNFIPTSVFTTDLQYVDFLDRVHKAELKLRSKNLWEVPHPWLNLFVPKSRISDFD


KGVFKGILGNKTSGPILIYPMNKDKWDERSSAVTPDEEVFYLVALLRSALTDGEETQKLEYLKDQNRRILEFCEQAKINVKQYLPHHATQEEWVAHFGD


KWDRFRSLKAEFDPRHILATGQRIFQNPSLSLFPPSSSSSSAASW*


 


Promoter Candidate ID: 15295988


 


Modulates the gene as identified by its GI number: 38605153


 


The GenBank description of the gene: Probable xyloglucan endotransglucosylase/hydrolase protein 15


precursor (At-XTH15) (XTH-15) >gi|1244760|gb|AAB18368.1| xyloglucan endotransglycosylase-related


protein >gi|15028017|gb|AAK76539.1|


 


The promoter sequence: (SEQ ID NO: 33)


gtcgacgctacaatgttgatttattggttgtggtttgcatcttggggatgtcaaatcctaagtttcaagttcttgtaaaaacgttttcaggtttcttta


atatattttaatattaatgtaaaaagaaaagatatagcttttgtacaaaaaaatttgtttaatcactatgtaggaggatgcgatcaaattcatggaatg


atgtattattagcttttctatcctcactctaaaaacaatactatagtgagttaaata


 


The Ceres cDNA ID of the endogenous coding sequence to the promoter: 12711515


 


cDNA nucleotide sequence: (nucleotides 1–255 of SEQ ID NO: 34)


ATCTCACACCAAAACACAAAGCTCTCATCTTCTTTTAGTTTCCAAACTCACCCCCACAACTTTCATTTCTATCAACCAAACCCAAATGGGTCCAAGTTC


GAGCCTCACCACCATCGTGGCGACTGTTCTTCTTGTGACATTGTTCGGTTCGGCCTACGCAAGCAACTTCTTCGACGAGTTTGACCTCACTTGGGGTGA


CCACAGAGGCAAAATCTTCAACGGAGGAAATATGCTGTCTTTGTCGCTGGACCAGGT


 


Coding sequence: (SEQ ID NO: 35)


MGPSSSLTTIVATVLLVTLFGSAYASNFFDEFDLTWGDHRGKIFNGGNMLSLSLDQVSGSGFKSKKEYLVGRIDMQLKLVAGNSAGTVTAYYLSSQGAT


HDEIDFEFLGNETGKPYVLHTNVFAQGKGDREQQFYLWFDPTKNFHTYSIVWRPQHIIFLVDNLPIRVFNNAEKLGVPFPKSQPMRIYSSLWNADDWAT


RGGLVKTDWSKAPFTAYYRGFNAAACTASSGCDPKFKSSFGDGKLQVATELNAYGRRRLRWVQKYFMIYNYCSDLKRFPRGFPPECKKSRV*


 


Promoter Candidate ID: 15295991


 


Modulates the gene as identified by its GI number: 15227116


 


The GenBank description of the gene: cytochrome P450, putative; protein id: At2g21910.1 [Arabidopsis


thaliana] >gi|25282629|pir||F84606 probable cytochrome P450 [imported] - Arabidopsis thanliana >gi|


4417283|gb|AAD20408.1| putative cytochrome P450 [Arabidopsis thaliana]


 


The promoter sequence: (SEQ ID NO: 36)


gattgaatgatgagtgtgcacccttgtattactaataaaaaatttagcaacagttataagctaacgtcatccatgagtcattcattagattcactattt


gcgttctcaaaaatcgaattgttaaaatttgagaagctctaatatacgagtcaatgagatgtggcaaaagcatgtccttgaccataaaatttcgagggg


tcaactcattagataaggacaagaatcaaccaattgaaggcgtcttctataacaagt


 


The Ceres cDNA ID of the endogenous coding sequence to the promoter: 12734860


 


cDNA nucleotide sequence: (nucleotides 1–255 of SEQ ID NO: 37)


ATGGCTTACGTAGGCTTAGTTGAAGTCTTTATTGCCTTACTTGTCTTTTTCTTCTTCCATTTCTTGATCCACAAGAAATCTCATCAAATCACACCTAGA


AACTGGCCAGTTCTTGGGATGCTTCCTGGTGTCCTTGTCATGCTTCACAGGATCAATGACTATGTCGCGGAGATTCTTGAGGTCTCCAACTTGACATTT


GCCTTCAAAGGCCCATGGTTCTCTGGAATGAACATGTTGATCACTGCAGATCCTTCA


 


Coding sequence: (SEQ ID NO: 38)


MAYVGLVEVFIALLVFFFFHFLIHKKSHQITPRNWPVLGMLPGVLVMLHRINDYVAEILEVSNLTFAFKGPWFSGMNMLITADPSNIQHVFSSNFSNYD


KGPEFKEMFDFLGNGIFTADSKLWEDMRKSALVVLSHQGFQSFSLRTITCKIKNGLVPVLDHFAEANTVFDLQDVFQRLAFDVTLTLVTGCDSSSLSIE


MPKNEYAKAMDDAEEVVVYRHVKPVVLWKLQNWIGLGEEKKMKEANAAFDRSCAKYISAKREEIISHHSNIGGEAHAEDLLSVYMNLDISKYELLNPND


DNFLKDIIKSFMLAGRDAIATTLTWFFWLLSKNPEAVTKIRQEINTNLPGSGMSLDADKLNKMVYLHGALCESLRLYAPIPFERKTPIKQDVLPSGHMV


DKNWKILFSVYALGRMRSVWGQDASEFKPERWISERNGGLKHEPSFKFFVFNSGPRNCLGKNLSFLQMKTVAVEIIRNYDIKVVEGHKIEPASSIILHM


KHGLKVTVSKRGLVS*


 


Promoter Candidate ID: 15295994


 


Modulates the gene as identified by its GI number: 18418018


 


The GenBank description of the gene: putative protein; protein id: At4g32460.1, supported by cDNA:


37529. [Arabidopsis thaliana] >gi|21593257|gb|AAM65206.1| unknown [Arabidopsis thaliana]


 


The promoter sequence: (SEQ ID NO: 39)


ttttcgaaaatttaaataatgattcgatcaacactttttctcattttatcaaacccctttgattgaatagaccgctaaaacaatttgcttgattggtct


ttcttacaacgactaagttacaaatgtgactgaaagttaccgatcaaacccatgaaaaaaacttgagcccatataccttgctatggatttggcacacag


accaagctttcgaagcaactgtttggttgattcggaattgttttctgataataaata


 


The Ceres cDNA ID of the endogenous coding sequence to the promoter: 12371508


 


cDNA nucleotide sequence: (nucleotides 1–255 of SEQ ID NO: 40)


ATTCCACTCCCACTAAACATTCCTTCTCTCGCTCACTCTTCTCCAATCCTTATTTTATTTTTTGAAAGTTTAAAATTTTATACAACATATCAATTTGGG


GTAGAAAAATTCGAAAGAAATGAAAGAGATGGGAGTGATAGTGCTTCTTCTCCTTCACTCGTTCTTCTACGTTGCCTTTTGCTTCAATGATGGACTACT


ACCAAACGGTGACTTCGAACTCGGTCCACGACATTCGGACATGAAAGGAACACAAGT


 


Coding sequence: (SEQ ID NO: 41)


MKEMGVIVLLLLHSFFYVAFCFNDGLLPNGDFELGPRHSDMKGTQVINITAIPNWELSGFVEYIPSGHKQGDMILVVPKGAFAVRLGNEASIKQKISVK


KGSYYSITFSAARTCAQDERLNVSVAPHHAVMPIQTVYSSSGWDLYSWAFKAQSDYADIVIHNPGVEEDPACGPLIDGVAMRALFPPRPTNKNILKNGG


FEEGPWVLPNISSGVLIPPNSIDDHSPLPGWMVESLKAVKYIDSDHFSVPQGRRAVELVAGKESAVAQVVRTIPGKTYVLSFSVGDASNACAGSMIVEA


FAGKDTIKVPYESKGKGGFKRSSLRFVAVSSRTRVMFYSTFYAMRNDDFSSLCGPVIDDVKLLSARRP*


 


Promoter Candidate ID: 15296000


 


Modulates the gene as identified by its GI number: 15234651


 


The GenBank description of the gene: hypothetical protein; protein id: At4g30180.1 [Arabidopsis


thaliana] >gi|7486762|pir||T14078 hypothetical protein F9N11.30 - Arabidopsis thaliana >gi|5730128|


mb|CAB52462.1| hypothetical hypothetical protein [Arabidopsis thaliana]


 


The promoter sequence: (SEQ ID NO: 42)


cgtcatattagttacagtggcagtaaaattcagtttcaaagatgtttgtcttgatatgttgtacagatcaccaattgaactaccactaataataactaa


atttctgtttagcaagttaccatctgtatccaaatatcgcaaaagtagtgggtagtgaaacccaaattcatcacacatgcagcataaaaaaaaagaagg


tcaaatggtatatataatatgagggagatctatattaagataatatgggtagaaatg


 


The Ceres cDNA ID of the endogenous coding sequence to the promoter: 12656661


 


cDNA nucleotide sequence: (SEQ ID NO: 43)


ATGGAGAGGCAAATCATAAACAGGAAGAAACGAGTGTTTTCTCTTGAACCAAACAAGAACCCTAGTGCAGTTTTCACGAGAAAATACACAAGCCACTTG


GTTCCTGCACTCAAGAAGCTCAACATGAACAAGAACTCTTCAAAACAAACCGTGAAGCATGAAGTAGATATGGCTTTGGCTTTGTCTGCTCAAGAATTT


GCATGGAGCCGTTTCTTGCTGCAGAAGCTATCGTCCTCATCGAATCCAACCACTACCACTAGTTCTTCTTCCGATGGAATTCGGATTCTTGAAAGACCC


GATAAAGAAGGCGGAAACGAAGAAGGAGGGATAGAGGAGAGACTGAGGGAATTGAAGAAGCTTTTGCCAGGTGGGGAAGAGATGAATGTGGAAGAAATG


TTGAGTGAGATTGGTAACTACATTAAATGTCTTGAGTTGCAGACGATTGCTCTCAAGTCCATTGTTCAAGATAGTACTTGA


 


Coding sequence: (SEQ ID NO: 44)


MERQIINRKKRVFSLEPNKNPSAVFTRKYTSHLVPALKKLNMNKNSSKQTVKHEVDMALALSAQEFAWSRFLLQKLSSSSNPTTTTSSSSDGIRILERP


DKEGGNEEGGIEERLRELKKLLPGGEEMNVEEMLSEIGNYIKCLELQTIALKSIVQDST*


 


Promoter Candidate ID: 15296003


 


Modulates the gene as identified by its GI number: 18403306


 


The GenBank description of the gene: Expressed protein; protein id: At3g22231.1, supported by cDNA:


gi_14335055 [Arabidopsis thaliana] >gi|14335056|gb|AAK59792.1| AT3g22240/MMP21_1 [Arabidopsis


thaliana] >gi|27363330|gb|AAO11584.1| At3g22240/MMP21_1 [Arabidopsis thaliana]


 


The promoter sequence: (SEQ ID NO: 45)


acagatcacaccaacataaggaacaaagccaaaactattaatcatggttcaaaggcagttggttaatcactttttcattttcatgaaatgttaaattaa


ttaatcatcaaaagaggttatttaatttacatagagtttagagcaatacccaaaaaaaaaaaaaagaggttctaaaagacagttccaggaacaaaataa


ttcaaatttgttaaattcctcatgttttacgacgtcatgtacgtgtacgtcatgtacgtgacgaaagccatttctgcaacaaaccatttctcactttca


tctcaaccataggtatcgctttcctctgcccttgtgcatttcaaacaatatcatttgctttatctctgcaattatatatgtgttggatataaccaaaaa


acctagacctaccacttcgctaaggtaggtctgtccgtgagttgtctgtgattagatgttttattgttcaatattgactcttctttcttttatataatg


aataatgtaaaaaatttcctaatatttgtctaccttataaattagaagcacaacactctctcctcttcacaaatctcacatcctcactcctcagctcct


caaatcaga


 


The Ceres cDNA ID of the endogenous coding sequence to the promoter: 12730017


 


cDNA nucleotide sequence: (SEQ ID NO: 46)


ACAAATCTCACATCCTCACTCCTCAGCTCCTCAAATCAGAATGAATCAATCCGCGCAAAATTACTTTTCCGTGCAAAAACCTTCAGAGACTTCATCAGG


GCCGTACACAAGTCCGCCACCAATTGGTTATCCGACTAGAGATGCGGTGGTGGGTGATCCTCCGGCAGCAGCAGTGGAGACAAACTCCAAGGGCGTCAA


CCCCGAAGCCATAATGAGTTGTTTTAGTACTTGTATGGAGTGTATCTTCTGCTGCGGCGTATGCTCCAGCCTCTGTACATCAGAGTAAATCAGCATGAT


GAGACAGAAGTCGTTGCCCAAACCTGAAAAACAACACGTGATAGAAAATCTATATATATATATATATATATATATGTTATAGTAGTCGTTTCTATGGAT


TTCCACGCATTTTAAAGTTTATTTGTTTCACTGTTTAAAATGAATCATTTGCTTCGTGTATTTTGTTTCTATAT


 


Coding sequence: (SEQ ID NO: 47)


MNQSAQNYFSVQKPSETSSGPYTSPPPIGYPTRDAVVGDPPAAAVETNSKGVNPEAIMSCFSTCMECIFCCGVCSSLCTSE*


 


Promoter Candidate ID: 15296006


 


Modulates the gene as identified by its GI number: 7487010


 


The GenBank description of the gene: hypothetical protein T14P8.2 - Arabidopsis thaliana >gi|3193289|


gb|AAC19273.1| similar to several small proteins (~100 aa) that are induced by heat, auxin,


ethylene and wounding such as Phaseolus aureus indole-3-acetic acid induced protein ARG


 


The promoter sequence: (SEQ ID NO: 48)


atcttgacatgcttaaacacattttataattcgaacctcactttgcctactttacacacgtctacttatagtagatgagcatcaatcattgaaccgttc


gtataatacaattttttttttgtaatacgttataattagaaagtaatggaaaataagttgaaacacaaattttcaacggttttactaagatttaatttt


tacaattttcaaaatataaccgaattatttaaatcgtattaaatttataattaatttt


 


The Ceres cDNA ID of the endogenous coding sequence to the promoter: 12339689


 


cDNA nucleotide sequence: (SEQ ID NO: 49)


TCATCTCTTCAAACCATTTTCGAAAGCCTTGAGAGAGAGAACACAGACGATACCAACTTTCTTCAATCTCGTTGCCGCAGTATAATTATCTCATTCCTC


GGATATATCTCTCCTTCTGCGGCGGCGACAAGAAGCTACAAGAATAAAAAGTCTGTTTTCTCTCTTTTCAAGAAACCACTTACTTCGAAAATGGCTCGT


TCTATCTCTAACGTTAAGATCGTATCTGCTTTCGTCTCTCGTGAACTCTCCAATGCTATCTTCCGACGTGGTTATGCGGCCACGGCGGCGCAAGGGAGC


GTTTCGAGCGGTGGAAGAAGTGGAGCTGTTGCTTCGGCTGTGATGAAGAAGAAGGGAGTGGAAGAATCAACCCAGAAGATTTCTTGGGTTCCAGATCCC


AAAACCGGTTATTACAGACCCGAAACCGGTTCCAACGAGATTGACGCGGCTGAGCTACGAGCAGCTCTCTTGAACAACAAGCAGTGATTGATTATTATT


ACATGTAATTTTGTCAAGGTCTTTAAGAGGAGATTAGTGGGTAATGATCTGGTGCAGTGAACCCTATTTTCATATGTTAAGTGCGGTTCTGTAATGAAT


AAAATAGAGAAGCGTTTGGTTTCCTCTAATTGTAACAAAAGGATCGTTGGATGTATGATAGAGTTTTTCTTATAAAACCATTTCAGAACTT


 


Coding sequence: (SEQ ID NO: 50)


MARSISNVKIVSAFVSRELSNAIFRRGYAATAAQGSVSSGGRSGAVASAVMKKKGVEESTQKISWVPDPKTGYYRPETGSNEIDAAELRAALLNNKQ*


 


Promoter Candidate ID: 15296009


 


Modulates the gene as identified by its GI number: 18423445


 


The GenBank description of the gene: expressed protein [Arabidopsis thaliana] >gi|28973707|gb|


AAO64170.1| unknown protein [Arabidopsis thaliana] >gi|29824227|gb|AAPO4074.1| unknown


protein [Arabidopsis thaliana]


 


The promoter sequence: (SEQ ID NO: 51)


caacaaacattcccttggagatttgagagattcatatcattaaatgcacttctcaatatacggagtattactaattaaaaccttatttcgagttctctc


aaacgtaacccatgcaaaaatggccccagagataagactttgatgagtctccacgtcactttctgatttcggcttttgtcccctaatctttcgacaac


attcgtctcgcaccccgacatttcccgggacctctgtctctccccctctctttctcct


 


The Ceres cDNA ID of the endogenous coding sequence to the promoter: 13578669


 


cDNA nucleotide sequence: (SEQ ID NO: 93)


TTGTTTTGTCTCAAACAAATTTCTCTGCACACACTCAACAACATATCCCATAACAAAAAAAAGCTATTAAAAAAAAAGAGAAGCAGCCATGGAAGAAGG


TAAGCAAGAAGCTTCAATGCCACTAGTTCCAATTGACAGCTTCTCTTACAGTTGGTTAGTTAACTTTCCTTCTTTAGAAGCTACCATTGATGATCATCA


TCAAACATACGAAGATTCATCTTCTTCTTCTTCCTTCATTGAGATGGATCCAAGATT


 


Coding sequence: (SEQ ID NO: 54)


MEEGKQEASMPLVPIDSFSYSWLVNFPSLEATIDDHHQTYEDSSSSSSFIEMDPRLPPSRRFFIKTSHESSFKFDNFVSFSDEDHSLVHADELFRDGYV


MPYRLKPTSAATEEESEPLDTTTSEKIDTRGLNSKPSPTSSRKLRRVSKWVLLKYLDFLTPLCKRLRRCRSAVTTGSIGMDSRIRVTTSCRSRVYSDEM


TSSPRISVADDYYWRRSCDSESSIYEAVLHCKKSFEK*
















TABLE 2





Promoter Reports for Results of Far Red Induction Experiments















Promoter Expression Report #152


Promoter Tested In: Arabidopsis thaliana, Wassilewskija (WS) ecotype


Spatial expression summary:








Flower
H stomata


Silique
H stomata


Rosette Leaf
H stomata H stipule


Primary Root
L epidermis L trichoblast H cortex L root hairs







Observed expression pattern:


T1 mature: Guard cell expression throughout inflorescence apex and carpels in early


flower buds.


T2 seedling: GFP expression specific within cortex cells overlaying lateral root


primordia and root hair producing epidermal cells.








Expected expression pattern:
Petiole


Selection Criteria:
Mutant lines







Gene: product = “tetratricopeptide repeat (TPR)-containing note = “contains Pfam


profile PF00515 TPR Domain; go function: protein binding [goid 0005515]”


GenBank: NM_129819 tetratricopeptide repeat (TPR)-containing protein (At2g42580) mRNA








Source Promoter Organism:
Arabidopsis thaliana, Columbia (Col) ecotype


Vector:
pNewbin4-HAP1-GFP


Marker Type:
GFP-ER







Generation Screened:  X T1 Mature X T2 Seedling ↑T2 Mature ↑T3 Seedling


Inductions completed.
















Events Screened/



Treatment:
Age:
Gen:
Time points:
Response
Response:


1. Drought
4 wks
T2
8 days no water
2/0
No


2. Far red
7 days
T2
 1 Hr
2/0
No


Far Red730 = 525 μW/cm2


 4 Hr
2/0
No





24 Hr
2/0
No







Inducible expression summary:










Treatment:
Time point induced:
Organs induced:
Tissues induced:








T1 Mature Plant Expression
Organs/Tissues screened










Events Screened:
n = 6
Events Expressing:
n = 2








GFP Expression



X Flower
↑pedicel ↑receptacle ↑nectary ↑sepal ↑petal ↑filament ↑anther ↑pollen



↑carpel ↑style ↑papillae ↑vascular ↑epidermis H stomata ↑trichome



↑silique


X Silique
↑stigma ↑style ↑carpel ↑septum ↑placentae ↑transmitting tissue ↑vascular



↑epidermis H stomata ↑abscission zone ↑ovule


 ↑ Ovule
Pre-fertilization: ↑primordia ↑inner integument ↑outer integument ↑embryo



sac ↑funiculus ↑chalaza ↑micropyle ↑gametophyte



Post-fertilization: ↑zygote ↑suspensor ↑ embryo sack ↑inner integument



↑outer integument ↑endothelium ↑seed coat ↑primordia ↑chalaza



↑micropyle ↑early endosperm ↑mature endosperm ↑embryo


  ↑ Embryo
↑suspensor ↑preglobular ↑globular ↑heart ↑torpedo ↑late ↑mature



↑provascular ↑hypophysis ↑radicle ↑cotyledons ↑hypocotyl


↑ Stem
↑epidermis ↑cortex ↑vascular ↑xylem ↑phloem ↑pith ↑stomata ↑trichome


↑ Leaf
↑petiole ↑mesophyll ↑vascular ↑epidermis ↑trichome ↑primordia ↑stomata



↑stipule ↑margin


↑ Shoot apical meristem
↑shoot apical meristem ↑flower primordium







X Guard cells (Gc) in Flower Bud, Pedicle and Silique








T2 Seedling Expression
Tissues Screened


Events Screened: n = 2
   Events Expressing: n = 2







Seedlings expressing/Seedlings screened


Event-01: 5/6


Event-02: 4/6


↑ Scheduled


GFP Expression Detected








↑ Hypocotyl
↑epidermis ↑cortex ↑vascular ↑xylem ↑phloem ↑stomata


↑ Cotyledon
↑mesophyll ↑vascular ↑epidermis ↑margin ↑stomata



↑hydathode


X Rosette Leaf
↑mesophyll ↑vascular ↑epidermis ↑trichome ↑petiole



↑primordia H stomata H stipule ↑margin ↑hydathode


X Primary Root
L epidermis L trichoblast ↑atrichoblast H cortex ↑endodermis



↑vascular ↑xylem ↑phloem ↑pericycle ↑quiescent



↑columella ↑root cap L root hairs


↑ Lateral root
↑epidermis ↑trichoblast ↑atrichoblast ↑cortex ↑endodermis



↑initials ↑flanking cells ↑vascular ↑lateral root cap


↑ Shoot apical meristem
↑Shoot apical meristem







X Cortex (Cr) in root transition zone, lateral root, and lateral root initial


X Epidermis (Ep) in lateral root, and root


X Guard cell (Gc) in seedling, rosette leaf


X Lateral root (Lr) in lateral root, lateral root initial


X Root hair (Rh) in root


X Stipules (Ss) in seedling,


Promoter utility








Trait Area:
  Water use efficiency, nutrients


Sub-trait Area:
  Heat, drought, water potential, moisture stress at seed set, moisture



  stress during seed fill, low nitrogen tolerance, nitrogen use efficiency


Utility:
Among other uses this promoter sequence could be useful to improve:


Notes:








Construct:
PT0590


Promoter candidate I.D:
11768848


cDNA I.D:
12639140 (OCKHAM3-CD)


Lines expressing:
PT0590-03, -04 Jan. 16, 2004









(A) Predicted promoter sequence (1000 bp).










5′ CCAGTCGA▾TTGGCCCGAT▾CGGCC NNNNNNNNNNNNNN GGCCTGCA▾GGGCCAGTGCA▾CTGG 3′
(SEQ ID NO: 2)



 


>152.PT0590 predicted
(SEQ ID NO: 55)


attattcaatttaataaaaattgagtcggccaatttaatgcgagacttctgtacaacgaccctaaaagtgggtttgat


 


aaatgaaacatattgcaacaaaaaaatactagtaataatgataaaatagtaacatgtcgtggcgcattgaatatccta


 


cgaaggtttagtgtttacttttaaaaaatcctaatatgatactagtacatatagctagcttgccttgcttatgctatt


 


gcatagtctgtattaataaatgatgttatacatttcgatagagtaacattttgggaacatgagtgaacgtgcttgaat


 


cttcgtgcccttgacgtcagaagctagtaattttaaatactaattaacattcatacaaattaacagatacaatgtact


 


atatcataattcgtttccgtaacacaacgcaacaatttgaaagtagatgtactttagtacttagttagtgtgcaccaa


 


aaaaaaaagatgtagttagttagtaaggggttaaatgttttaatttattaagaaaacttaaattcattaaatgttaga


 


aaaagtctaattagtttatattcgaacactgtgctcaaaattaaaaagtcaactattttagactatagagtttattaa


 


ttaataataaattcgataaatcaccgtattattttcttcaacgacaagtagccgtgaagacacgggagcgaagagaga


 


taaacagaagatgaagaagaagatcaatgtcataatcttcagggagataaatccgtaatctttattaatcaaggttaa


 


tccttttttttttcttcatcttaattctttgcgtcttccttttctatttatcacgagatctgtctttctttttcctct


 


tctttctctctcttctctctgaagacagtacttgtttctgtccggcgttaaaagcttcggtggtggtctcttgacttc


 


tctgagaagaagaaaaggaagctgagtctcattttagattcagctcacgaggaagtgacgacga






(B) Sequence verification and confirmation.










>152.PT0590 experimental
(SEQ ID NO: 94)



tcgattggcccgatcggccattattcaatttaataaaaattgagtcggccaatttaatgcgagacttctgtacaacgaccct


 


aaaagtgggtttgataaatgaaacatattgcaacaaaaaaatactagtaataatgataaaatagtaacatgtcatggcgcat


 


tgaatatcctacgaaggtttagtgtttacttttaaaaaatcctaatatgatactagtacatatagctagcttgccttgctta


 


tgctattgcatagtctgtattaataaatgatgttatacatttcgatagagtaacattttgggaacatgagtgaacgtgcttg


 


aatcttcgtgcccttgacgtcagaagctagtaattttaaatactaattaacattcatacaaattaacagatacaatgtacta


 


tatcataattcgtttccgtaacacaacgcaacaatttgaaagtagatgtactttagtacttagttagtgtgcaccaaaaaaa


 


aagatgtagttagttagtaaggggttaaatgttttaatttattaagaaaacttaaattcattaaatgttagaaaaagtctaa


 


ttagtttatattcgaacactgtgctcaaaattaaaaagtcaactattttagactatagagtttattaattaataataaattc


 


gataaatcaccgtattattttcttcaacgacaagtagccgtgaagacacgggagcgaagagagataaacagaagatgaagaa


 


gaagatcaatgtcataatcttcagggagataaatccgtaatctttattaatcaaggttaatccttttttttttcttcatctt


 


aattctttgcgtcttccttttctatttatcacgagatctgtctttctttttcctcttctttctctctcttctctctgaagac


 


agtacttgtttctgtccggcgttaaaagcttcggtggtggtctcttgacttctctgagaagaagaaaaggaagctgagtctc


 


attttagattcagctcacgaggaagtgacgacgaggcctgcagggccagtgcactgggatccaacaatgtcctccgactcgt


 


ccaagatcaagaggaagcggaaccgcatcccg


















Sequence (bp)
Mismatch
Predicted/Experimental







138
Ecotype variant
g/a







Sequence Q.C. notes:









(C) Predicted vs. Experimental sequence alignment.













Score = 1902 bits (989), Expect = 0.0


Identities = 999/1000 (99%), Gaps = 1/1000 (0%)


Query = Predicted (SEQ ID NO: 55)


Subject = Experimental (nucleotides 20–1018 of SEQ ID NO: 94)


 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 

























Promoter Expression Report #171















Promoter Tested In: Arabidopsis thaliana, Wassilewskija (WS) ecotype


Spatial expression summary:








Ovule
   Post-fertilization: H suspensor H inner integument L mature endosperm


Embryo
H suspensor


Hypocotyl
   H vascular


Cotyledon
   L hydathode


Primary Root
H vascular







Observed expression pattern:


T1 mature: GFP expressed in endothelium cell layer of maturing ovules and in depleted


endosperm cells of maturing seed. No expression observed in endosperm of developing


ovules.


T2 seedling: High GFP expression throughout vasculature of root and hypocotyl. Weak GFP


expression in hydathodes of cotyledons.








Expected expression pattern:
   Shade Induced


Selection Criteria:
   Microarray


Gene:
    Auxin-responsive AUX/IAA family protein







GenBank: NM_119380 Arabidopsis thaliana auxin-responsive AUX/IAA family protein


(At4g32280) mRNA, complete cds gi |30689330|ref|NM_119380.2|[30689330]








Source Promoter Organism:
   Arabidopsis thaliana, Columbia (Col) ecotype


Vector:
   pNewbin4-HAP1-GFP


Marker Type:
  GFP-ER







Generation Screened:  XT1 Mature XT2 Seedling ↑T2 Mature ↑T3 Seedling


Inductions completed.
















Events Screened/



Treatment:
Age:
Gen:
Time points:
Response
Response:


1. Far red
7 days
T2
 1 Hr
2/0
No


Far Red730 = 525 μW/cm2


24 Hr
2/0
No







Inducible expression summary:










Treatment:
Time point induced:
Organs induced:
Tissues induced:








1. Far red
No differences observed.







Far Red730 = 525 μW/cm2








T1 Mature Plant Expression
Organs/Tissues screened










Events Screened:
n = 2
Events Expressing:
n = 2







GFP Expression Detected








↑ Flower
↑pedicel ↑receptacle ↑nectary ↑sepal ↑petal ↑filament ↑anther ↑pollen



↑carpel ↑style ↑papillae ↑vascular ↑epidermis ↑stomata ↑trichome



↑silique


↑ Silique
↑stigma ↑style ↑carpel ↑septum ↑placentae ↑transmitting tissue ↑vascular



↑epidermis ↑stomata ↑abscission zone ↑ovule


 X Ovule
Pre-fertilization: ↑primordia ↑inner integument ↑outer integument ↑embryo



sac ↑funiculus ↑chalaza ↑micropyle ↑gametophyte



Post-fertilization: ↑zygote H suspensor ↑embryo sack H inner integument



↑outer integument ↑endothelium ↑seed coat ↑primordia ↑chalaza



↑micropyle ↑early endosperm L mature endosperm ↑embryo


  ↑ Embryo
H suspensor ↑preglobular ↑globular ↑heart ↑torpedo ↑late ↑mature



↑provascular ↑hypophysis ↑radicle ↑cotyledons ↑hypocotyl


↑ Stem
↑epidermis ↑cortex ↑vascular ↑xylem ↑phloem ↑pith ↑stomata ↑trichome


↑ Leaf
↑petiole ↑mesophyll ↑vascular ↑epidermis ↑trichome ↑primordia ↑stomata



↑stipule ↑margin


↑ Shoot apical meristem
↑shoot apical meristem ↑flower primordium







X Endosperm (En) in the ovule, developing seed coat, mature ovule/early seed


X Endothelium (Ed) in the ovule, developing seed coat, and mature ovule/early seed


X Seed coat (Sc) in the developing seed coat


X Suspensor (Su) in the mature ovule/early seed








T2 Seedling Expression
Tissues Screened


Events Screened: n = 2
   Events Expressing: n = 2







Seedlings expressing/Seedlings screened


Event 01: 2(4)


Event 02: 5(6)


GFP Expression Detected








X Hypocotyl
↑epidermis ↑cortex H vascular ↑xylem ↑phloem ↑stomata


X Cotyledon
↑mesophyll ↑vascular ↑epidermis ↑margin ↑stomata L hydathode


↑ Rosette Leaf
↑mesophyll ↑vascular ↑epidermis ↑trichome ↑petiole ↑primordia



↑stomata ↑stipule ↑margin ↑hydathode


X Primary Root
↑epidermis ↑trichoblast ↑atrichoblast ↑cortex ↑endodermis H vascular



↑xylem ↑phloem ↑pericycle ↑quiescent ↑columella ↑root cap ↑root hairs


↑ Lateral root
↑epidermis ↑trichoblast ↑atrichoblast ↑cortex ↑endodermis ↑initials



↑flanking cells ↑vascular ↑lateral root cap


↑ Shoot apical meristem
↑shoot apical meristem







X Hydathode (Hd) in the cotyledon


X Vascular (Vs) in the cotyledon, and root


Induction Screens








1. Far red
No differences observed. Images not shown.







Far Red730 = 525 μW/cm2








Promoter utility



Trait Area:
PG&D, nutrients


Sub-trait Area:
Nitrogen use efficiency, yield, seed size


Nominated By:
Shing Kwok


Investigators:
Medrano, L., Theiss, N.


Utility:
Among other uses this promoter sequence could be useful to modulate



seed size and nitrogen use efficiency.


Construct:
  PT0672


Promoter candidate I.D:
15295940


cDNA I.D:
23523314, 12655184 (OCKHAM3-CD)


Lines expressing:
PT0672-01, -02









(A) Predicted promoter sequence (1000 bp).










5′ CCAGTCGA▾TTGGCCCGAT▾CGGCC NNNNNNNNNNNNNN GGCCTGCA▾GGGCCAGTGCA▾CTGG 3′
(SEQ ID NO: 2)



 


>171.PT0672 predicted
(SEQ ID NO: 58)


cagccgtaaatccttccataaatttattttgcaagttttgctcattatataatgagcggaatttatgatataatcgtt


 


tgtaataatgttatgttttgatcaaaatttgaaattaaaagtaggtgagaacttgttatacagtgtagataaggtgga


 


tcttgaatataaaaataaaatttataagatgtatttaaagcagaaaagcataaaactttagataaaataatgtaaaaa


 


tgtgttagcatcaatgttgggatattggccgacccgaacttaatcaatgtcggaagccattacttctctcccaaaaga


 


cctttttccttcggagaactaggaacttcctcactacctttcgcttaacgtgaaagccataaatttcatatattcata


 


aaaatcagaaaatctaaaactgtttagtatcacctgtttttggtatagactattggttttgtgttacttcctaaacta


 


tatgatttcgtacttcattggatcttatagagatgaatattcgtaaaaagataagttatctggtgaaacgttacttca


 


gtcatgttgggtctagatttacatactactatgaaacattttaagataataattatcctagccaactatatgttctat


 


attatgggccaagaagatatagaactaaaagttcagaatttaacgatataaattactagtatattctaatacttgaat


 


gattactgttttagttgtttagaataaatagtagcgtgttggttaagataccatctatccacatctatatttgtgtgg


 


gttacataaaatgtacataatattatatacatatatatgtatatttttgataaagccatatattactccttgacctct


 


gcccccatttccttttactataaataggaatactcatgatcctctaattcagcaatcaacaccaacgaacacaacctt


 


ttccaaagccaataataaaagaacaaaagcttttagtttcatcaaagacgaagctgccttagaa






(B) Sequence verification.









(SEQ ID NO: 59)









>171.PT0672 experimental



cagccgtaaatcctccataaatttattttgcaagttttgctcattatata


 


atgagcggaatttatgatataatcgtttgtaataatgttatgttttgatc


 


aaaatttgaaattaaaagtaggtgagaacttgttatacagtgtagataag


 


gtggatcttgaatataaaaataaaatttataagatgtatttaaagcagaa


 


aagcataaaactttagataaaataatgtaaaaatgtgttagcatcaatgt


 


tgggatattggccgacccgaacttaatcaatgtcggaagccattacttct


 


ctcccaaaagacctttttccttcggagaactaggaacttcctcactacct


 


ttcgcttaacgtgaaagccataaatttcatatattcataaaaatcagaaa


 


atctaaaactgtttagtatcacctgtttttggtatagactattggttttg


 


tgttacttcctaaactatatgatttcgtacttcattggatcttatagaga


 


tgaatattcgtaaaaagataagttatctggtgaaacgttacttcagtcat


 


gttgggtctagatttacatactactatgaaacattttaagataataatta


 


tcctagccaactatatgttctatattatgggccaagaagatatagaacta


 


aaagttcagaatttaacgatataaattactagtatattctaatacttgaa


 


tgattactgttttagttgtttagaataaatagtagcgtgttggttaagat


 


accatctatccacatctatatttgtgtgggttacataaaatgtacataat


 


attatatacatatatatgtatatttttgataaagccatatattactcctt


 


gacctctgcccccatttccttttactataaataggaatactcatgatcct


 


ctaattcagcaatcaacaccaacgaacacaaccttttccaaagccaataa


 


taaaagaacaaaagcttttagtttcatcaaagacgaagctgccttagaa


















Predicted Position (bp)
Mismatch
Predicted/Experimental







15
SNP
t/—







Sequence Q.C.:









(C) Predicted vs. Experimental sequence alignment.













Query = Predicted (SEQ ID NO: 58)


Subject = Experimental (SEQ ID NO: 59)


Score = 1894 bits (985), Expect = 0.0


Identities = 999/1001 (99%), Gaps = 2/1001 (0%)


Strand = Plus/Plus


 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 

























Promoter Expression Report # 175















Promoter Tested In: Arabidopsis thaliana, Wassilewskija (WS) ecotype


Spatial expression summary:








Ovule
L chalaza


Leaf
L vascular


Cotyledon
L epidermis


Primary Root
H vascular







Observed expression pattern:


T1 mature: GFP expressed in vascular tissues of leaf and in funiculus-ovule connective site.


T2 seedling: GFP expression in root vascular tissue.








Expected expression pattern:
   Shade induced


Selection Criteria:
    Microarray


Gene:
    hypothetical protein







GenBank: NM_119287 Arabidopsis thaliana hypothetical protein (At4g31380) mRNA, complete cds gi|


18417796|ref|NM_119287.1|[18417796]








Source Promoter Organism:
   Arabidopsis thaliana, Columbia (Col) ecotype


Vector:
   pNewbin4-HAP1-GFP


Marker Type:
  GFP-ER







Generation Screened:  XT1 Mature XT2 Seedling ↑T2 Mature ↑T3 Seedling


Inductions completed.
















Events Screened/



Treatment:
Age:
Gen:
Time points:
Response
Response:


1. Far Red
7 days
T2
 1 Hr
2/1
Yes


Far Red730 = 525 μW/cm2


24 Hr
2/0
No


2. Far Red
7 days
T2
 1 Hr
3/0
No


Far Red730 = 525 μW/cm2


24 Hr
3/0
No







Inducible expression summary:










Treatment:
Time point induced:
Organs induced:
Tissues induced:


1. Far Red
1 Hr
Rosette leaf
Epidermal


2. Far Red
No response observed.








T1 Mature Plant Expression
Organs/Tissues screened










Events Screened:
n = 5
Events Expressing:
n = 2







GFP Expression Detected








↑ Flower
↑pedicel ↑receptacle ↑nectary ↑sepal ↑petal ↑filament ↑anther ↑pollen



↑carpel ↑style ↑papillae ↑vascular ↑epidermis ↑stomata ↑trichome



↑silique


↑ Silique
↑stigma ↑style ↑carpel ↑septum ↑placentae ↑transmitting tissue ↑vascular



↑epidermis ↑stomata ↑abscission zone ↑ovule


 X Ovule
Pre-fertilization: ↑primordia ↑inner integument ↑outer integument ↑embryo



sac ↑funiculus ↑chalaza ↑micropyle ↑gametophyte



Post-fertilization: ↑zygote ↑suspensor ↑ embryo sack ↑inner integument



↑outer integument ↑endothelium ↑seed coat ↑primordia L chalaza



↑micropyle ↑early endosperm ↑mature endosperm ↑embryo


  ↑ Embryo
↑suspensor ↑preglobular ↑globular ↑heart ↑torpedo ↑late ↑mature



↑provascular ↑hypophysis ↑radicle ↑cotyledons ↑hypocotyl


↑ Stem
↑epidermis ↑cortex ↑vascular ↑xylem ↑phloem ↑pith ↑stomata ↑trichome


X Leaf
↑petiole ↑mesophyll L vascular ↑epidermis ↑trichome ↑primordia ↑stomata



↑stipule ↑margin


↑ Shoot apical meristem
↑ Shoot apical meristem ↑ Flower primordium







X Chalaza (Ch) in the ovule


X Funiculus (Fn) in the ovule


X Micropyle (Mp) in the ovule


X Vascular (Vs) in the leaf








T2 Seedling Expression
Tissues Screened


Events Screened: n = 2
Events Expressing: n = 2







Seedlings expressing/Seedlings screened


Event-03: 2(6)


Event-05: 3(6)








GFP Expression Detected



↑ Hypocotyl
↑epidermis ↑cortex ↑vascular ↑xylem ↑phloem ↑stomata


X Cotyledon
↑mesophyll ↑vascular L epidermis ↑margin ↑stomata



↑hydathode


↑ Rosette Leaf
↑mesophyll ↑vascular ↑epidermis ↑trichome ↑petiole



↑primordia ↑stomata ↑stipule ↑margin ↑hydathode


X Primary Root
↑epidermis ↑trichoblast ↑atrichoblast ↑cortex ↑endodermis



H vascular ↑xylem ↑phloem ↑pericycle ↑quiescent ↑columella ↑root



cap ↑root hairs


↑ Lateral root
↑epidermis ↑trichoblast ↑atrichoblast ↑cortex ↑endodermis



↑initials ↑flanking cells ↑vascular ↑lateral root cap


↑ Shoot apical meristem
↑Shoot apical meristem







X Epidermis (Ep) in the colyledon


X Hypocotyl (Hy) in the root


X Vascular (Vs) in the root








Promoter utility



Trait Area:
PG&D, source


Sub-trait Area:
Seed size, low light tolerence, increased germination


Nominated By:
Shing Kwok


Investigators:
Medrano, L., Theiss, N.


Utility:
Among other uses this promoter sequence could be useful to modulate



seed size and shade avoidance







Notes: 1) There is one knock-out allele in the Salk collection for this locus.








Construct:
  PT0673


Promoter candidate I.D:
  15295943


cDNA I.D:
23416553, 13618832


Lines expressing:
PT0673-03, -05









(A) Predicted promoter sequence (1000 bp).










5′ CCAGTCGA▾TTGGCCCGAT▾CGGCC NNNNNNNNNNNNNN GGCCTGCA▾GGGCCAGTGCA▾CTGG 3′
(SEQ ID NO: 2)



 


>175.PT0673 predicted
(SEQ ID NO: 60)


tgtttttcatttttttttcatttcgttactactaacagaacttttcatttatatcttgaaattttgttgtataactca


 


aataaagattgaaactaacatgatgatacttgtaattatctgattatttccttccatgtaaaccgatcaacatctagt


 


cgtaaaacagaaaacaaaaaagacactgatcgacactcatagcataacaaccgatcttagtatacatatgtgtgatat


 


gttacgtcatatttagctcatgcaaactagaatttcttgccgtatttcagttccatatatctcggatatgcatatcaa


 


atttacgacaagaatctaaattttgtgaaatattaccaaagattcctttatatatagaaaagagataaattaaccaca


 


caaacataataaaatggaaaaagaagaagagattcgaaaatgtggacccattttttaaaaattctaacattcaaactg


 


aataaatttcccacgctaattttgatttatttatctccttgcatatcggaataagtataacattcttcaaagaccaaa


 


aaaagaagaaagtataatattctttcaatcaatttccatagaaaagatatggcatttcaattacgtcccaaatatgac


 


gatcgaaatcatcttatataactcaaagtatttaactacatatagtttcgaatcagaaaaatagctttggttttacgg


 


attttgagttatgctcttgtgtcaaaatatgataaataaattgttggtagattgatagataagattcttccttttcga


 


aaattctggaattctgcatttaatatatatatatatatcatataatataatgataatctacttgtcagtctacacacc


 


cctttaccaacatatatatatatatatagcacacactctacacggtttccttatcctcatcaaaattaacaaactcat


 


ttttgaatacccaaaaaaaaacctagctagctcgaatttttttaaatatataataacatcaaca






(B) Sequence verification.








(SEQ ID NO: 61)








>175.PT0673 experimental



tgtttttcatttttttttcatttcgttactactaacagaacttttcattt


 


atatcttgaaattttgttgtataactcaaataaagattgaaactaacatg


 


atgatacttgtaattatctgattatttccttccatgtaaaccgatcaaca


 


tccagtcgtaaaacagaaaacaaaaaagacactgatcgacactcatagca


 


taacaaccgatcttagtatacatatgtgtgatatgttacgtcatatttag


 


ctcatgcaaactagaatttcttgccgtatttcagttccatatatctcgga


 


tatgcatatcaaatttacgacaagaatctaaattttgtgaaatattacca


 


aagattcctttatatatagaaaagagataaattaaccacacaaacataat


 


aaaatggaaaaagaagaagagattcgaaaatgtggacccattttttaaaa


 


attctaacattcaaactgaataaatttcccacgctaattttgatttattt


 


atctccttgcatatcggaataagtataacattcttcaaagaccaaaaaaa


 


gaagaaagtataatattctttcaatcaatttccatagaaaagatatggca


 


tttcaattacgtcccaaatatgacgatcgaaatcatcttatataactcaa


 


agtatttaactacatatagtttcgaatcagaaaaatagctttggttttac


 


ggattttgagttatgctcttgtgtcaaaatatgataaataaattgttggt


 


agattgatagataagattcttccttttcgaaaattctggaattctgcatt


 


taatatatatatatatatcatataatataatgataatctacttgtcagtc


 


tacacacccctttaccaacatatatatatatatatagcacacactctaca


 


cggtttccttatcctcatcaaaattaacaaactcatttttgaatacccaa


 


aaaaaaacctagctagctcgaatttttttaaatatataataacatcaaca


















Predicted Position (bp)
Mismatch
Predicted/Experimental







153
SNP
t/c







Sequence Q.C.:









(C) Predicted vs. Experimental sequence alignment.













(Query: SEQ ID NO: 60)


(Subject: SEQ ID NO: 61)


Score = 1917 bits (997), Expect = 0.0


Identities = 999/1000 (99%)


Strand = Plus/Plus


 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 

























Promoter Expression Report #176















Promoter Tested In: Arabidopsis thaliana, Wassilewskija (WS) ecotype


Spatial expression summary:








Flower
  H pedicel H sepal H petal H filament M carpel M style H epidermis M silique


Silique
  M style M carpel H epidermis L ovule


Ovule
  Post-fertilization: L outer integument


Embryo
M heart M torpedo M late


Stem
  H vascular H pith


Hypocotyl
  H epidermis


Cotyledon
  H epidermis


Rosette Leaf
  M epidermis


Primary Root
M epidermis L root hairs


Lateral root
M epidermis







Observed expression pattern:


T1 mature: GFP expressed throughout mature plant. In the flower, GFP is first expressed in young buds


at the pedicles and sepals, later in the mature flower, GFP expression extends to the sepals, petals,


and silique. GFP is not expressed in the anthers or stigma. High GFP expression is observed in heart


stage through mature embryos. Weak expression in outer integument of some ovules. High GFP


expression throughout vascular and pith regions of stem.


T2 seedling: High GFP expression throughout epidermal cells of seedling. No expression in root caps


or guard cells. 








Expected expression pattern:
   Shade Induced


Selection Criteria:
    Microarray


Gene:
    allergen V5/Tpx-1-related family protein







GenBank: NM_126057 Arabidopsis thaliana allergen V5/Tpx-1-related family protein (At5g66590)


mRNA, complete cds gi|30698237|ref|NM_126057.2|[30698237]








Source Promoter Organism:
   Arabidopsis thaliana, Columbia ecotype


Vector:
   pNewbin4-HAP1-GFP


Marker Type:
  GFP-ER







Generation Screened:  XT1 Mature XT2 Seedling ↑T2 Mature ↑T3 Seedling


Inductions completed.
















Events Screened/



Treatment:
Age:
Gen:
Time points:
Response
Response:


1. Far red
7 days
T2
 1 Hr
5/0
No


Far Red730 = 525 μW/cm2


24 Hr
5/0
No







Inducible expression summary:










Treatment:
Time point induced:
Organs induced:
Tissues induced:









1. Far red
1 Hr, 24 Hr
No differences observed.








T1 Mature Plant Expression
Organs/Tissues screened










Events Screened:
n = 6
Events Expressing:
n = 5







GFP Expression Detected








X Flower
H pedicel ↑receptacle ↑nectary H sepal H petal H filament ↑anther ↑pollen



M carpel M style ↑papillae ↑vascular H epidermis ↑stomata ↑trichome



M silique


X Silique
↑stigma M style M carpel ↑septum ↑placentae ↑transmitting tissue



↑vascular H epidermis ↑stomata ↑abscission zone L ovule


 X Ovule
Pre-fertilization: ↑primordia ↑inner integument ↑outer integument ↑embryo



sac ↑funiculus ↑chalaza ↑micropyle ↑gametophyte



Post-fertilization: ↑zygote ↑suspensor ↑ embryo sack ↑inner integument



L outer integument ↑endothelium ↑seed coat ↑primordia ↑chalaza



↑micropyle ↑early endosperm ↑mature endosperm ↑embryo


  X Embryo
↑suspensor ↑preglobular ↑globular M heart M torpedo M late ↑mature



↑provascular ↑hypophysis ↑radicle ↑cotyledons


X Stem
↑epidermis ↑cortex H vascular ↑xylem ↑phloem H pith ↑stomata



↑trichome


↑ Leaf
↑petiole ↑mesophyll ↑vascular ↑epidermis ↑trichome ↑primordia ↑stomata



↑stipule ↑margin


↑ Shoot apical meristem
↑shoot apical meristem ↑flower primordium







X Anther (An) in the mature flower


X Carpel (Ca) in the silique and mature ovule


X Embryo (Em) in the mature ovule


X Filament (Fi) in the mature flower


X Petal (Pe) in the mature flower


X Pith (Pi) in the stem


X Sepal (Se) in the developing flower


X Silique (Si) in the developing flower


X Ovules (Ov) in the mature ovule


X Vascular bundle (Vb) in the stem








T2 Seedling Expression
Tissues Screened








Events Screened: n = 2
Events Expressing: n = 2







Seedlings expressing/Seedlings screened


Event-01: 4(6)


Event-02: 5(6)








GFP Expression Detected



X Hypocotyl
H epidermis ↑ cortex ↑vascular ↑xylem ↑phloem ↑stomata


X Cotyledon
↑mesophyll ↑vascular H epidermis ↑margin ↑stomata ↑hydathode


X Rosette Leaf
↑mesophyll ↑vascular M epidermis ↑trichome ↑petiole ↑primordia



↑stomata ↑stipule ↑margin ↑hydathode


X Primary Root
M epidermis ↑trichoblast ↑atrichoblast ↑ cortex ↑endodermis



↑vascular ↑xylem ↑phloem ↑pericycle ↑quiescent ↑columella ↑root cap



L root hairs


X Lateral root
M epidermis ↑trichoblast ↑atrichoblast ↑cortex ↑endodermis ↑initials



↑flanking cells ↑vascular ↑lateral root cap


↑ Shoot apical meristem
↑shoot apical meristem







X Epidermis (Ep) in the cotyledon and roots


X Guard cells (Gc) in the cotyledon


X Hypocotyl (Hy) in the seedling and cotyledon


X Rosette leaf (Rl) in the seedling


X Root hair (Rh) in the roots








Promoter utility



Trait Area:
PG&D, nutrients, cold


Sub-trait Area:
Seed size, nitrogen use efficiency, cold tolerance


Utility:
Among other uses this promoter sequence could be useful to modulate







seed size, nitrogen use efficiency, and cold tolerance in seedlings. Nitrogen inducible expression in broad


range of tissues can be useful for improving tolerance to low nitrogen.








Construct:
  PT0681


Promoter candidate I.D:
  15295979


cDNA I.D:
23541268 (12688858)


Lines expressing:
PT0681-01, -03, -04, -05, -06









(A) Predicted promoter sequence (1000 bp).










5′ CCAGTCGA▾TTGGCCCGAT▾CGGCC NNNNNNNNNNNNNN GGCCTGCA▾GGGCCAGTGCA▾CTGG 3′
(SEQ ID NO: 2)



 


>176.PT0681 predicted
(SEQ ID NO: 62)


gactttttttttatggagaacaaattatccagtagatgtttttttttattgctcagtaattgagaaatgggcacgagg


 


atgaagatattccattgatgtgattccaatcttaataacattgcaatttcgtagctatataaatcatttcatgtgtaa


 


tattatccatcttgttaaattttctaatctctaaaatttcataccgtttgtgtttaacatagtttccgatccaatcca


 


atccagcaaagtgaaataatttcgaatgataaggctgttttgcaaaatgccaaatatggcggaacaatttttatttaa


 


gaaacaagataaggattattaatgatcagatatgcttgatgaagttgtggtccattcttacttctcttctgcatattt


 


atcacatcggtttctcattatctctatgcattcgggactactaatacaacaatagcacaaaaatacaacgtgacaaca


 


aaaacaaccgagtagaaaactataaagacaacaacatttcaaattctctgttgccactaatactgaaaatccatttaa


 


attttctttttgtgggttgaatttgcaccatataaaaatccaataatacaaaagaaagcaaatatacatgattggata


 


ttcttcgattatgatgtcgaacaacaacaattattaacatgtgtatagtttggcaaaaaatgaatatgaggtaaagag


 


ggctggacccattggccctataagcattaatgggcctgaaagcaacaacagaaattggaattaaataacgttgggtat


 


ctgtctgtcacatgcaacacagacaacttgagaatggatcaatcaacattcacgtgccatgatcctctcttcctctta


 


ttttgtctccttccaccaatcccatatctttctctattatacatctctaattatctcacttttaacatatagtttttt


 


tatacatctttaatgactatataaaccaaacactgatctttttcaggttgcgaataaaccaaga






(B) Sequence verification.









(SEQ ID NO: 63)









>176.PT0681 experimental



gactttttttttatggagaacaaattatccagtagatgtttttttttatt


 


gctcagtaattgagaaatgggcacgaggatgaagatattccattgatgtg


 


attccaatcttaataacattgcaatttcgtagctatataaatcatttcat


 


gtgtaatattatccatcttgttaaattttctaatctctaaaatttcatac


 


cgtttgtgtttaacatagtttccgatccaatccaatccagcaaagtgaaa


 


taatttcgaatgataaggctgttttgcaaaatgccaaatatggcggaaca


 


atttttatttaagaaacaagataaggattattaatgatcagatatgcttg


 


atgaagttgtggtccattcttacttctcttctgcatatttatcacatcgg


 


tttctcattatctctatgcattcgggactactaatacaacaatagcacaa


 


aaatacaacgtgacaacaaaaacaaccgagtagaaaactataaagacaac


 


aacatttcaaattctctgttgccactaatactgaaaatccatttaaattt


 


tctttttgtgggttgaatttgcaccatataaaaatccaataatacaaaag


 


aaagcaaatatacatgattggatattcttcgattatgatgtcgaacaaca


 


acaattattaacatgtgtatagtttggcaaaaaatgaatatgaggtaaag


 


agggctggacccattggccctataagcattaatgggcctgaaagcaacaa


 


cagaaattggaattaaataacgttgggtatctgtctgtcacatgcaacac


 


agacaacttgagaatggatcaatcaacattcacgtgccatgatcctctct


 


tcctcttattttgtctccttccaccaatcccatatctttctctattatac


 


atctctaattatctcacttttaacatatagtttttttatacatctttaat


 


gactatataaaccaaacactgatctttttcaggttgcgaataaaccaaga


















Predicted Position (bp)
Mismatch
Predicted/Experimental







1–1000
None








Sequence Q.C.









(C) Predicted vs. Experimental sequence alignment.













Score = 1923 bits (1000), Expect = 0.0


Identities = 1000/1000 (100%)


Strand = Plus/Plus


Query = Predicted (SEQ ID NO: 62)


Subject = Experimental (SEQ ID NO: 63)


 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 

























Promoter Expression Report #177















Promoter Tested In: Arabidopsis thaliana, Wassilewskija (WS) ecotype


Spatial expression summary:








Flower
  H pedicel H petal M filament M anther H epidermis H carpel


Silique
H carpel H epidermis


Stem
  L endodermis H pith


Rosette Leaf
  L epidermis H trichome H petiole







Observed expression pattern:


T1 mature: Vegetatative expression. GFP expressed in epidermis of stem and pedicels of the


inflorescence meristem near the shoot apex. In the Flower, GFP expression is specific to stamen


and carpels of siliques. GFP highly expressed in parenchyma cells of stem. No expression in ovules.


T2 seedling: High specific GFP expression in cells at the base of developing trichomes and petioles


of rosette leaves. Expression in adventitious trichome cells of the hypocotyls.








Expected expression pattern:
Shade Induced


Selection Criteria:
    Ceres expression data


Gene:
    expressed protein; “/product = “unknown protein”







GenBank: NM_113862 expressed protein (At3g29370) mRNA, complete








Source Promoter Organism:
   Arabidopsis thaliana, Columbia ecotype


Vector:
   pNewbin4-HAP1-GFP


Marker Type:
  GFP-ER







Generation Screened:  XT1 Mature XT2 Seedling ↑T2 Mature ↑T3 Seedling


Inductions completed.
















Events Screened/



Treatment:
Age:
Gen:
Time points:
Response
Response:


1. Far red
7 days
T2
 1 Hr
2/0
No


Far Red730 = 525 μW/cm2


24 Hr
2/1
Yes







Inducible expression summary:










Treatment:
Time point induced:
Organs induced:
Tissues induced:


1. Far red
24 Hr
Petiole
Epidermis, Cortex, Vascular








Far Red730 = 525 μW/cm2



T1 Mature Plant Expression
Organs/Tissues screened










Events Screened:
n = 6
Events Expressing:
n = 2








GFP Expression Detected



X Flower
H pedicel ↑receptacle ↑nectary ↑sepal H petal M filament M anther



↑pollen H carpel ↑style ↑papillae ↑vascular H epidermis ↑stomata



↑trichome ↑silique


X Silique
↑stigma ↑style H carpel ↑septum ↑placentae ↑transmitting tissue ↑vascular



H epidermis ↑stomata ↑abscission zone ↑ovule


 ↑ Ovule
Pre-fertilization: ↑primordia ↑inner integument ↑outer integument ↑embryo



sac ↑funiculus ↑chalaza ↑micropyle ↑gametophyte



Post-fertilization: ↑zygote ↑suspensor ↑ embryo sack ↑funiculus ↑inner



integument ↑outer integument ↑endothelium ↑seed coat ↑primordia ↑chalaza



↑micropyle ↑early endosperm ↑mature endosperm ↑embryo


  ↑ Embryo
↑suspensor ↑preglobular ↑globular ↑heart ↑torpedo ↑late ↑mature



↑provascular ↑hypophysis ↑radicle ↑cotyledons ↑hypocotyl


X Stem
↑ epidermis ↑cortex L endodermis ↑ vascular ↑xylem ↑phloem H pith



↑stomata ↑trichome


↑ Leaf
↑petiole ↑mesophyll ↑vascular ↑epidermis ↑trichome ↑primordia ↑stomata



↑stipule ↑margin


↑ Shoot apical meristem
↑ Shoot apical meristem ↑ Flower primordium







X Stem (Sm) in the inflorescence meristem


X Silique (Si) in the flower and silique


X Stamen (St) in the flower


X Ovule/Ovary (Ov) in the silique and ovary


X Pedicles (Pd) in the inflorescence meristem


X Pith (Pi) in the stem








T2 Seedling Expression
Tissues Screened








Events Screened: n = 2
Events Expressing: n = 2







Seedlings expressing/Seedlings screened


Event-01: 4(6)


Event-05: 3(6)


↑ No GFP Expression Detected








↑ Hypocotyl
↑epidermis ↑cortex ↑vascular ↑xylem ↑phloem ↑stomata


↑ Cotyledon
↑mesophyll ↑vascular ↑epidermis ↑margin ↑stomata



↑hydathode


X Rosette Leaf
↑mesophyll ↑vascular L epidermis H trichome H petiole



↑primordia ↑stomata ↑stipule ↑margin ↑hydathode


↑ Primary Root
↑epidermis ↑trichoblast ↑atrichoblast ↑cortex ↑endodermis



↑vascular ↑xylem ↑phloem ↑pericycle ↑quiescent



↑columella ↑root cap ↑root hairs


↑ Lateral root
↑epidermis ↑trichoblast ↑atrichoblast ↑cortex ↑endodermis



↑initials ↑flanking cells ↑vascular ↑lateral root cap


↑ Shoot apical meristem
↑Shoot apical meristem







X Epidermis (Ep) in the cotyledon


X Trichiomes (Tc) in the rosette leaf


X Petiole (Pt) in the seedling


Promoter utility


Trait Area:


Sub-trait Area:








Utility:
Among other uses this promoter sequence could be useful to


improve:
 Modulation of flower and inflorescence structure, especially


numbers of
  flowers per inflorescence and therefore seeds per


inflorescence.
   Modulation of carpel symmetry and number of


valves per carpel and
   number of seeds per carpel. Modulation of shade


avoidance responses,
   especially petiole and leaf elongation under


shade. Enhanced seedling
    and plant performance under shade


conditions. Combinational effects or
     growth, development, fertility and


responses to shade.


Notes:








Construct:
  PT0684


Promoter candidate I.D:
  15295997


cDNA I.D:
13486695


Lines expressing:
  PT0684-01-05; Apr. 26, 2004









(A) Predicted promoter sequence (1000 bp).









(SEQ ID NO: 64)









5′ CCAGTCGA▾TTGGCCCGAT▾CGGCC-tagctagatttctatataaac



 


agaagaaagttaaaaagcaaataaaaattcacaaatagaaatcgaacaaa


 


aagctatgaaaatataaataccataaccttatggaaaaacgatgaaatgc


 


ttaacaaaaaaaactttggcaatggcatgcatgtgcctgtaacagaaggc


 


ccccataagctgttagtgatatacaacttaagcaaatgtgcactcttcac


 


gcacttcccgcttttctaaatttcaatttatttgtctacatttttgtcca


 


aattattgatataattctaccacgacttcccccacatgtccctccaaaga


 


gatccgtactacacagtctaccgacagcacatgcatggattttccaaacc


 


atcttctttaaggataatccttgacatttttaatattaaaaaaataacaa


 


aaaattcaatatataaataacatcctaaatctatgttttggtagaaaaca


 


agttctaaagttcacatttggacagtggttagtacttggtaatcaaaata


 


tttgtttaagaatcttgactacttacttagtctaaaccctaacgtacatg


 


gttagacatattagacacaattctattctatagcttcttaacaaacgttt


 


agcataatccgaaattggttttaccaatatttattaccgtacgtgtgttt


 


ttttctgtaagaaaggaaaaaaagccaactcatgattcttctgatattgc


 


atgtaatatatttgccaaataagcttacgacacaaacacaatgacactat


 


gacagtaagatatcatttcaaaatacggatatacccccaaattggtggca


 


atgacaaagaaaaaaagagttcttcacagtggcacattcgtaatacatat


 


gaactttggtggttgtttcgtaatatagatcgtacttaaaacctctaaac


 


accgttctctttatttgccatcttcttcattatcatcatctccatctctc


 


tctctctctctctcattttcttgaaaaag-


 


GGCCTGCAVGGGCCAGTGCAVCTGG 3′






(B) Sequence verification and confirmation.













Sequence (bp)
Mismatch
Predicted/Experimental







415
SNP
a/—







Sequence Q.C. notes:









(C) Predicted vs. Experimental sequence alignment.













Score = 1892 bits (984), Expect = 0.0


Identities = 999/1000 (99%), Gaps = 1/1000 (0%)


Strand = Plus/Plus


Query = Predicted (nucleotides 24–1024 of SEQ ID NO: 64)


Subject = Experimental (nucleotides 24–1024 of SEQ ID NO: 65)


 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 

























Promoter Expression Report #178















Promoter Tested In: Arabidopsis thaliana, Wassilewskija (WS) ecotype


Spatial expression summary:








Flower
  H stomata


Ovule
  Post-fertilization: M endothelium


Stem
  H stomata


Leaf
  H stomata


Cotyledon
  H stomata


Rosette Leaf
  H stomata


Primary Root
M epidermis H pericycle H root hairs


Lateral root
H initials H lateral root cap







Observed expression pattern:


T1 mature: High GFP expression in guard cells throughout mature plant aerial tissue and endothelium


cell layer of developing seed.


T2 seedling: GFP expression in trichomes and guard cells of cotyledons and rosette leaves. Primary


expression in root localized to pericycle cells and lateral root initials and later in mature lateral root


cap. Weak epidermal and root hair expression.








Expected expression pattern:
   Shade Induced


Selection Criteria:
   Ceres expression data


Gene:
    short-chain dehydrogenase/reductase (SDR) family protein,



    oxidoreductase activity







GenBank: NM_120332 Arabidopsis thaliana short-chain dehydrogenase/reductase (SDR)


family protein (At5g02540) mRNA, complete cds gi|30679675|ref|NM_120332.2|[30679675]








Source Promoter Organism:
   Arabidopsis thaliana, Columbia


Vector:
   pNewbin4-HAP1-GFP


Marker Type:
  GFP-ER







Generation Screened: XT1 Mature XT2 Seedling ↑T2 Mature ↑T3 Seedling


Inductions completed:
















Events Screened/



Treatment:
Age:
Gen:
Time points:
Response
Response:


1. Far red
7 days
T2
 1 Hr
2/0
No


Far Red730 = 525 μW/cm2


24 Hr
2/2
Yes







Inducible expression summary:










Treatment:
Time point induced:
Organs induced:
Tissues induced:


1. Far red
 1 Hr
No differences observed.
Stomata (guard cells)


Far Red730 = 525 μW/cm2
24 Hr
Cotyledon
Stomata (guard cells)




Rosette Leaf








T1 Mature Plant Expression
Organs/Tissues screened










Events Screened:
n = 4
Events Expressing:
n = 2







GFP Expression Detected








X Flower
↑pedicel ↑receptacle ↑nectary ↑sepal ↑petal ↑filament ↑anther ↑pollen



↑carpel ↑style ↑papillae ↑vascular ↑epidermis H stomata ↑trichome



↑silique


↑ Silique
↑stigma ↑style ↑carpel ↑septum ↑placentae ↑transmitting tissue ↑vascular



↑epidermis ↑stomata ↑abscission zone ↑ovule


 X Ovule
Pre-fertilization: ↑primordia ↑inner integument ↑outer integument ↑embryo



sac ↑funiculus ↑chalaza ↑micropyle ↑gametophyte



Post-fertilization: ↑zygote ↑suspensor ↑embryo sack ↑inner integument



↑outer integument M endothelium ↑seed coat ↑primordia ↑chalaza



↑micropyle ↑early endosperm ↑mature endosperm ↑embryo


  ↑ Embryo
↑suspensor ↑preglobular ↑globular ↑heart ↑torpedo ↑late ↑mature



↑provascular ↑hypophysis ↑radicle ↑cotyledons ↑hypocotyl


X Stem
↑epidermis ↑cortex ↑vascular ↑xylem ↑phloem ↑pith H stomata ↑trichome


X Leaf
↑petiole ↑mesophyll ↑vascular ↑epidermis ↑trichome ↑primordia H stomata



↑stipule ↑margin


↑ Shoot apical meristem
↑shoot apical meristem ↑flower primordium







X Endothelium (Ed) in the developing seed


X Embryo (Em) in the developing seed


X Endosperm (En) in the developing seed


X Guard cell (Gc) in the inflorescence meristem and the leaf








T2 Seedling Expression
Tissues Screened








Events Screened: n = 2
Events Expressing: n = 2







Seedlings expressing/Seedlings screened


Event-03: 6(6)


Event-04: 5(6)


GFP Expression Detected








↑ Hypocotyl
↑epidermis ↑cortex ↑vascular ↑xylem ↑phloem ↑stomata


X Cotyledon
↑mesophyll ↑vascular ↑epidermis ↑margin H stomata



↑hydathode


X Rosette Leaf
↑mesophyll ↑vascular ↑epidermis ↑trichome ↑petiole



↑primordia H stomata ↑stipule ↑margin ↑hydathode


X Primary Root
M epidermis ↑trichoblast ↑atrichoblast ↑cortex ↑endodermis



↑vascular ↑xylem ↑phloem H pericycle ↑quiescent



↑columella ↑root cap H root hairs


X Lateral root
↑epidermis ↑trichoblast ↑atrichoblast ↑cortex ↑endodermis



H initials ↑flanking cells ↑vascular H lateral root cap


↑ Shoot apical meristem
↑shoot apical meristem







X Epidermis (Ep) in the root


X Guard cell (Gc) in the cotyledon


X Lateral root initial (Lri) in the lateral root initial


X Pericycle (Pr) in the root


X Root cap (Rc) in the lateral root cap


X Root hair (Rh) in the root


X Trichome (Tc) in the leaf








Promoter utility



Trait Area:
Stress, Nitrogen, PG&D


Sub-trait Area:
Drought, drought, nitrogen uptake, root architecture


Utility:
Among other uses this promoter sequence could be useful to



improve: Tolerance to drought conditions. Tolerance to heat



conditions. Modulation of responses to abiotic stress. Modulation of



plant interactions with insects and protection against insects.



Modulation of production and loading of volatiles into trichomes and



other epidermal cells. Enhanced root rate and root size. Modulation of



water and mineral ion uptake. Modulation of lateral root initiation and



growth and root architecture.








Construct:
  PT0678


Promoter candidate I.D:
  15295964


cDNA I.D:
12712683 (OCKHAM3-CD)


Lines expressing:
PT0678-03, -04









(A) Predicted promoter sequence (1000 bp).









(SEQ ID NO: 66)









5′ CCAGTCGA▾TTGGCCCGAT▾CGGCC-aattaaatgaaactcgcccct



 


aaattaggagggatttgggtaagtggtaacacattcactggaaacatgtg


 


aagaaaggaggatgtcaagtagctgaaaactcagtatagtaaccaacggc


 


ttctcaccaacctttcattaataatttggtcatccctatatttttattca


 


acattttgtttttcaatagcttagagcaccttaatacctttcagtgtttt


 


tttataaaaaaaaacaaaaattgggattaatcatcaatccccaaatgtaa


 


cgtttacttagattatgttcatttttctatacacacaaatcatattcttt


 


tgttttaatcttcgaaaaacgagaggacattaaatacccctaaaaaagga


 


ggggacattactaccaacgtacattaacatgtttgatagcaaacgattta


 


ttttgttcgttttgaaaaggggaaagtaatgtgtaaattatgtaaagatt


 


aataaacttttatggtatagtaacattttcgaataataagagagggaaaa


 


cactcgccattgtcggcaatttagaaccaatattagaagggtttttttag


 


agaaaaaggacttaaaagtttagagaccttaacaacaacttatttagaaa


 


tagacatgcttaagttgacaacagcgagtttattttctatatcgaagaaa


 


aatacgaactttttcttaattagatttcgaatgcatgcactatcgagaat


 


cgaccgtcacaagaaaaaactaatatacatactgtacatatctatattca


 


atattggtggggatgggtttaatgtgtatttataattcatggataaattc


 


acacaataaggtccatgaaactagaaggtaccaaaaataagcattaatga


 


ctctttgccacttatatatatgattctctcatagtaccattttattctcc


 


caaacctatcttcttcttcctctcttgtctctctcgctctctctcttcta


 


cattgtttcttgaggtcaatctattaaaa-


 


GGCCGATC▾GGGCCAATCGA▾CTGG 3′






(B) Sequence verification.













Predicted Position (bp)
Mismatch
Predicted/Experimental







 14 bp
SNP
t/—


235 bp
SNP
a/—







Sequence Q.C notes.









(C) Predicted vs. Experimental sequence alignment.













(Query: nucleotides 24–1024 of SEQ ID NO: 66)


(Subject: nucleotides 24–1021 of SEQ ID NO: 67)


Score = 1892 bits (984), Expect = 0.0


Identities = 998/1000 (99%), Gaps = 2/1000 (0%)


 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 

























Promoter Expression Report #193















Promoter Tested In: Arabidopsis thaliana, Wassilewskija (WS) ecotype


Spatial expression summary:








Flower
  H pedicel H receptacle L sepal H filament H carpel H epidermis H silique


Silique
H carpel H epidermis H abscission zone H ovule


Ovule
  Post-fertilization: H seed coat H embryo


Embryo
L torpedo H late H mature H radicle L cotyledons


Stem
  H epidermis H vascular


Leaf
  H vascular L epidermis


Cotyledon
  L epidermis


Rosette Leaf
  H epidermis H primordia


Primary Root
  L epidermis H vascular







Observed expression pattern:


T1 mature: GFP expressed in the inflorescence meristem, developing flower buds, mature flowers,


embryos, seed coats of mature ovules, stem and leaves. At the inflorescence meristem, GFP is


expressed throughout the stem and pedicels and sepals of developing flower buds. In mature


flowers, GFP is expressed in pedicels, siliques, and filaments of stamens. In ovules, GFP


expressed in mature or developing seed coats and embryos. GFP is expressed throughout


torpedo stage embryo, and later is preferentially expressed in root cap of developing radicle.


Weakly expressed in shoot apical meristem cells of embryo. GFP expressed in epidermal


and vasculature cells of leaf and stem.


T2 seedling: High GFP expression at the shoot apex and root vasculature of seedlings. High


GFP expression throughout epidermal cells of rosette leaves. Not expressed in guard cells.


High GFP expression in vasculature of root near root transition zone decreasing toward root


tip. Weak root epidermal expression.








Expected expression pattern:
   Microarray


Selection Criteria:
   Shade Induced


Gene:
    expressed protein (At3g22231)







GenBank: NM_113121 Arabidopsis thaliana expressed protein (At3g22231) mRNA,


complete cds gi|42565114|ref|NM_113121.3| [42565114]








Source Promoter Organism:
   Arabidopsis thaliana, Columbia (Col) ecotype


Vector:
   pNewbin4-HAP1-GFP


Marker Type:
  GFP-ER







Generation Screened:  XT1 Mature XT2 Seedling ↑T2 Mature ↑T3 Seedling


Inductions completed.
















Events Screened/



Treatment:
Age:
Gen:
Time points:
Response
Response:


1. Far red
7 days
T2
 1 Hr
5/2
Yes


Far Red730 = 525 μW/cm2


24 Hr
5/2
Yes







Inducible expression summary:










Treatment:
Time point induced:
Organs induced:
Tissues induced:


1. Far red
 1 Hr
Rosette leaf
Epidermis




Petioles
Epidermis



24 Hr
Rosette leaf
Epidermis




Petioles
Epidermis








T1 Mature Plant Expression
Organs/Tissues screened










Events Screened:
n = 4
Events Expressing:
n = 3








GFP Expression Detected



X Flower
H pedicel H receptacle ↑nectary L sepal ↑petal H filament ↑anther ↑pollen



H carpel ↑style ↑papillae ↑vascular H epidermis ↑stomata ↑trichome



H silique


X Silique
↑stigma ↑style H carpel ↑septum ↑placentae ↑transmitting tissue ↑vascular



H epidermis ↑stomata H abscission zone H ovule


 X Ovule
Pre-fertilization: ↑primordia ↑inner integument ↑outer integument ↑embryo



sac ↑funiculus ↑chalaza ↑micropyle ↑gametophyte



Post-fertilization: ↑zygote ↑suspensor ↑ embryo sack ↑funiculus ↑inner



integument ↑outer integument ↑endothelium H seed coat ↑primordia



↑chalaza ↑micropyle ↑early endosperm ↑mature endosperm H embryo


  X Embryo
↑suspensor ↑preglobular ↑globular ↑heart L torpedo H late H mature



↑provascular ↑hypophysis H radicle L cotyledons ↑root meristem ↑shoot



meristem


X Stem
H epidermis ↑ cortex H vascular ↑xylem ↑phloem ↑pith ↑stomata



↑trichome


X Leaf
↑petiole ↑mesophyll H vascular L epidermis ↑trichome ↑primordia



↑stomata ↑stipule ↑margin


↑ Shoot apical meristem
↑shoot apical meristem ↑flower primordium







X Anther (An) in the flower


X Chalaza (Ch) in the ovule


X Cotyledon (Co) in the ovule and embryo


X Cortex (Cr) in the stem


X Epidermis (Ep) in the inflorescence meristem, embryo, leaf and stem


X Filament (Fi) in the flower


X Flower (Fl) in the inflorescence meristem and flower


X Micropyle (Mp) in the ovule


X Ovule (Ov) in the ovule


X Pedicel (Pd) in the inflorescence meristem and flower


X Root cap (Rc) in the ovule and embryo


X Radicle (Rd) in the ovule


X Sepal (Se) in the flower


X Silique (Si) in the flower


X Shoot apical meristem (SAM) in the ovule


X Seed coat (Sc) in the ovule


X Vascular (Vs) in the flower and leaf


X Vascular bundle (Vb) in the stem








T2 Seedling Expression
Tissues Screened








Events Screened: n = 2
Events Expressing: n = 2







Seedlings expressing/Seedlings screened


Event-01: 5/6


Event-02: 3/6


↑ No GFP Expression Detected








↑ Hypocotyl
↑epidermis ↑cortex ↑vascular ↑xylem ↑phloem ↑stomata


X Cotyledon
↑mesophyll ↑vascular L epidermis ↑margin ↑stomata



↑hydathode


X Rosette Leaf
↑mesophyll ↑vascular H epidermis ↑trichome ↑petiole



H primordia ↑stomata ↑stipule ↑margin ↑hydathode


X Primary Root
L epidermis ↑trichoblast ↑atrichoblast ↑cortex ↑endodermis



H vascular ↑xylem ↑phloem ↑pericycle ↑quiescent



↑columella ↑root cap ↑root hairs


↑ Lateral root
↑epidermis ↑trichoblast ↑atrichoblast ↑cortex ↑endodermis



↑initials ↑flanking cells ↑vascular ↑lateral root cap


↑ Shoot apical meristem
↑shoot apical meristem







X Cotyledon (Co) in the seedling


X Hypocotyl (Hy) in the seedling


X Guard cell (Gc) in the rosette leaf


X Leaf (Lf) in the seedling


X Root hair (Rh) in the seedling


X Vascular (Vs) in the seedling








Promoter utility



Trait Area:
PG&D


Sub-trait Area:
Shade avoidance, seed size


Utility:
Among other uses this promoter sequence could be useful to modulate



shade avoidance and seed size







Notes: 1) A very short gene and there are no TAIL hits in either the Salk or Ceres population.








Construct:
  PT0859


Promoter candidate I.D:
  15296003


cDNA I.D:
23513118


Lines expressing:
  PT0859-01, 02, 05









FIG. 1. (A) Predicted promoter region was PCR amplified from the Columbia ecotype of A. thaliana. Cloned promoter fragment shown with linker sequence containing BstXI and SfiI (▾) sites at both 5′ and 3′ in uppercase bold letters. (B) Promoter construct sequence is 5′ verified in T1 mature plants and confirmed in the following generation by 5′and 3′ sequencing of the entire promoter of two or 3 events. Sequences from all events are used to generate a consensus sequence. In every case, the sequences of the 2–3 events have matched. Nucleotide discrepancies between predicted and experimental consensus sequences are verified by manual inspection of chromatographs and shown in accompanying table. (C) Alignment of the experimental consensus sequence from transgenic lines versus the predicted promoter sequence is shown below.
(A) Predicted promoter sequence (604 bp).









5′ CCAGTCGA▾TTGGCCCGAT▾CGGCC NNNNNNNNNNNNNN GGCCTGCA▾GGGCCAGTGCA▾CTGG 3′
(SEQ ID NO: 2)



 


>193.PT0859 predicted
(SEQ ID NO: 68)


acagatcacaccaacataaggaacaaagccaaaactattaatcatggttcaaaggcagttggttaatcactttttcat


 


tttcatgaaatgttaaattaattaatcatcaaaagaggttatttaatttacatagagtttagagcaatacccaaaaaa


 


aaaaaaaagaggttctaaaagacagttccaggaacaaaataattcaaatttgttaaattcctcatgttttacgacgtc


 


atgtacgtgtacgtcatgtacgtgacgaaagccatttctgcaacaaaccatttctcactttcatctcaaccataggta


 


tcgctttcctctgcccttgtgcatttcaaacaatatcatttgctttatctctgcaattatatatgtgttggatataac


 


caaaaaacctagacctaccacttcgctaaggtaggtctgtccgtgagttgtctgtgattagatgtttttattgttcaa


 


tattgactcttctttcttttatataatgaataatgtaaaaaatttcctaatatttgtctaccttataaattagaagca


 


caacactctctcctcttcacaaatctcacatcctcactcctcagctcctcaaatcaga






(B) Sequence verification and confirmation.









(SEQ ID NO: 69)









>193.PT0859 experimental



acagatcacaccaacataaggaacaaagccaaaactattaatcatggttc


 


aaaggcagttggttaatcactttttcattttcatgaaatgttaaattaat


 


taatcatcaaaagaggttatttaatttacatagagtttagagcaataccc


 


aaaaaaaaaaaaaagaggttctaaaagacagttccaggaacaaaataatt


 


caaatttgttaaattcctcatgttttacgacgtcatgtacgtgtacgtca


 


tgtacgtgacgaaagccatttctgcaacaaaccatttctcactttcatct


 


caaccataggtatcgctttcctctgcccttgtgcatttcaaacaatatca


 


tttgctttatctctgcaattatatatgtgttggatataaccaaaaaacct


 


agacctaccacttcgctaaggtaggtctgtccgtgagttgtctgtgatta


 


gatgtttttattgttcaatattgactcttctttcttttatataatgaata


 


atgtaaaaaatttcctaatatttgtctaccttataaattagaagcacaac


 


actctctcctcttcacaaatctcacatcctcacccctcagctcctcaaat


 


caga


















Sequence (bp)
Mismatch
Predicted/Experimental







584
SNP
t/c







Sequence Q.C. notes:









(C) Predicted vs. Experimental sequence alignment.













Query = Predicted (SEQ ID NO: 68)


Subject = Experimental (SEQ ID NO: 69)


Score = 1156 bits (601), Expect = 0.0


Identities = 603/604 (99%)


Strand = Plus/Plus


 








 








 








 








 








 








 








 








 








 








 

























Promoter Expression Report #203















Promoter Tested In: Arabidopsis thaliana, Wassilewskija (WS) ecotype


Spatial expression summary:








Hypocotyl
L stomata


Cotyledon
L stomata


Rosette Leaf
L stomata


Primary Root
L epidermis H endodermis







Observed expression pattern:


T1 mature: No expression observed.


T2 seedling: Primary GFP expression in root endodermal cell layer with weak expression in


epidermal cells near transition zone. Guard cell expression throughout aerial tissue.








Expected expression pattern:
   Shade Induced


Selection Criteria:
    Ceres expression data


Gene:
    Expressed protein







GenBank: NM_125622 Arabidopsis thaliana expressed protein (At5g62280) mRNA, complete cds


gi|30697652|ref|NM_125622.2|[30697652]








Source Promoter Organism:
   Arabidopsis thaliana, Columbia


Vector:
   pNewbin4-HAP1-GFP


Marker Type:
  GFP-ER







Generation Screened:  XT1 Mature XT2 Seedling ↑T2 Mature ↑T3 Seedling


Inductions completed:
















Events Screened/



Treatment:
Age:
Gen:
Time points:
Response
Response:


1. Far red
7 days
T2
 1 Hr
2/0
No


Far Red730 = 525 μW/cm2


24 Hr
2/0
No







Inducible expression summary:










Treatment:
Time point induced:
Organs induced:
Tissues induced:









1. Far red
 1 Hr
No differences observed.


Far Red730 = 525 μW/cm2
24 Hr
No differences observed.







Observation note: No differences were observed between control and experimental seedlings under


far red conditions. Difference in expression levels compared to original T2 seedling screen. Higher


expression can be seen in root epidermal cells and no GFP in guard cells can be detected.








T1 Mature Plant Expression
Organs/Tissues screened










Events Screened:
n = 3
Events Expressing:
n = 0







X No GFP Expression Detected








T2 Seedling Expression
Tissues Screened








Events Screened: n = 2
Events Expressing: n = 2







Seedlings expressing/Seedlings screened


Event-01: 2/6


Event-04: 2/6


GFP Expression Detected








X Hypocotyl
↑epidermis ↑cortex ↑vascular ↑xylem ↑phloem L stomata


X Cotyledon
↑mesophyll ↑vascular ↑epidermis ↑margin L stomata



↑hydathode


X Rosette Leaf
↑mesophyll ↑vascular ↑epidermis ↑trichome ↑petiole



↑primordia L stomata ↑stipule ↑margin ↑hydathode


X Primary Root
L epidermis ↑trichoblast ↑atrichoblast ↑cortex H endodermis



↑vascular ↑xylem ↑phloem ↑pericycle ↑quiescent



↑columella ↑root cap ↑root hairs


↑ Lateral root
↑epidermis ↑trichoblast ↑atrichoblast ↑cortex ↑endodermis



↑initials ↑flanking cells ↑vascular ↑lateral root cap


↑ Shoot apical meristem
↑shoot apical meristem







X Cortex (Cr) in the root


X Endodermis (Eo) in the root


X Epidermis (Ep) in the seedling


X Guard cells (Gc) in the seedling


X Vascular bundle (Vb) in the root








Promoter utility



Trait Area:
Stress, nutrients


Sub-trait Area:
Drought, nitrogen uptake


Utility:
Among other uses this promoter sequence could be useful to



improve: Modulation of all responses to drought and heat stress.



Protection against drought stress. Protection against heat stress.


Notes:
Endogenous promoter is down-regulated in heat and drought, up-



regulated in far red light and circadian rhythm.








Construct:
  PT0679


Promoter candidate I.D:
  15295967


cDNA I.D:
12732583 (OCKHAM3-CD)


Lines expressing:
PT0679-01









FIG. 1. (A) Predicted promoter region was PCR amplified from the Columbia ecotype of A. thaliana. Cloned fragment shown with primer sequence underlined and linkers containing BsTXI and Sfi I (▾) sites at both 5′ and 3′ in uppercase bold letters. (B) Promoter construct sequence is 5′ verified in T1 mature plants and confirmed in the following generation by 5′ and 3′ sequencing of the entire promoter of two or 3 events. Sequences from all events are used to generate a consensus sequence. In every case, the sequences of the 2–3 events have matched. Nucleotide discrepancies between predicted and experimental consensus sequences are verified by manual inspection of chromatographs and shown in accompanying table. (C) Alignment of the experimental consensus sequence from transgenic lines versus the predicted promoter sequence is shown below.
(A) Predicted promoter sequence (1000 bp).








5′ CCAGTCGA▾TTGGCCCGAT▾CGGCCtaagaaaaactgtaggcttgtt



 


gtcagaacaaacatggacccatgttctctatgtccctaagatgtgtacca


 


atctcaattcacttcttttgttgcactattttttaaaaaataacttttat


 


tttatattttgagatctccattgcccctgctgcactagacattacagctc


 


attttttccttataattcaatccctagctatttttctttcttattagttt


 


aaactaatcatatttgggtaattagcgttgaaactatctatcatatcaat


 


tttaatgatacatatgcaatactttatgtgagtatatgcatgtatgcatg


 


ttccaacatccagattaatgactaacgtttaagccctgattttttcagag


 


aaattttgtgttgtacctatgtttgtattacacacaatatttaccattgt


 


ttaacatgtacacatgtgtttataaatctccgtacactataatgcatatt


 


tgaaccatatatgacagaaagttttccactagttctaattacattttgtt


 


gccctttcctactcgtctattgcctatagaaatattattttagttatgat


 


taagaattgggatgcacattccgaaattaattattaaatgccactatgaa


 


gaacccttgaacatagtctaattcaattttaagatcataaggaacattaa


 


cagtgacaatagctaaggtctctcgacaatgagacaatccgctttttaaa


 


tatatacatataagagataccatattgtatacatatgcagatacaattac


 


aacttgaccaaatttattcaatttctccttctctttatatcaataagaaa


 


ctattcatgatactggaccagcctgtttgaatcttgtcccatccacaaat


 


ctcccaatatataaataaagaaccttcacccgtaaaaccaaaaccatcaa


 


caacttcaaagctttctaagcaagagattgagagaaatcggattttcttt


 


ctaagactcaaaatatctaaaaacaataGGCCTGCA▾GGGCCAGTGCA▾


 


CTGG 3′






(B) Sequence verification and confirmation.













Sequence (bp)
Mismatch
Predicted/Experimental







1–1000
none
1000/1000 (100%)







Sequence Q.C. notes:









(C) Predicted vs. Experimental sequence alignment.













Query = Predicted (nucleotides 24–1023 of SEQ ID NO: 57)


Subject = Experimental (nucleotides 24–1023 of SEQ ID NO: 57)


Score = 1923 bits (1000), Expect = 0.0


Identities = 1000/1000 (100%)


 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 

























Promoter Expression Report #204















Promoter Tested In: Arabidopsis thaliana, Wassilewskija (WS) ecotype


Spatial expression summary:








Cotyledon
   M hydathode


Primary Root
H epidermis H root hairs







Observed expression pattern:


T1 mature: No expression.


T2 seedling: GFP predominately expressed throughout root epidermal cells. Highest at


GFP expression near hypocotyl root transition zone decreasing toward root tip.








Expected expression pattern:
   Shade Induced


Selection Criteria:
    Microarray


Gene:
    zinc finger (CCCH-type) family protein







GenBank: NM_123793 Arabidopsis thaliana zinc finger (CCCH-type) family protein


(At5g44260) mRNA, complete cds gi |30694483|ref|NM_123793.2|[30694483]








Source Promoter Organism:
   Arabidopsis thaliana, Columbia (Col) ecotype


Vector:
   pNewbin4-HAP1-GFP


Marker Type:
  GFP-ER







Generation Screened:  XT1 Mature XT2 Seedling ↑T2 Mature ↑T3 Seedling


Inductions completed.
















Events Screened/



Treatment:
Age:
Gen:
Time points:
Response
Response:


1. Far red
7 days
T2
 1 Hr
2/0
No


Far Red730 = 525 μW/cm2


24 Hr
2/0
No







Inducible expression summary:










Treatment:
Time point induced:
Organs induced:
Tissues induced:


1. Far red
No differences observed.


Far Red730 = 525 μW/cm2








T1 Mature Plant Expression
Organs/Tissues screened










Events Screened:
n = 3
Events Expressing:
n = 0







X No GFP Expression Detected








T2 Seedling Expression
Tissues Screened








Events Screened: n = 2
Events Expressing: n = 2







Seedlings expressing/Seedlings screened


Event-01: 5/6


Event-02: 5/6


GFP Expression Detected








↑ Hypocotyl
↑epidermis ↑cortex ↑vascular ↑xylem ↑phloem ↑stomata


X Cotyledon
↑mesophyll ↑vascular ↑epidermis ↑margin ↑stomata



M hydathode


↑ Rosette Leaf
↑mesophyll ↑vascular ↑epidermis ↑trichome ↑petiole



↑primordia ↑stomata ↑stipule ↑margin ↑hydathode


X Primary Root
H epidermis ↑trichoblast ↑atrichoblast ↑cortex ↑endodermis



↑vascular ↑xylem ↑phloem ↑pericycle ↑quiescent



↑columella ↑root cap H root hairs


↑ Lateral root
↑epidermis ↑trichoblast ↑atrichoblast ↑cortex ↑endodermis



↑initials ↑flanking cells ↑vascular ↑lateral root cap


↑ Shoot apical meristem
↑shoot apical meristem







X Epidermis (Ep) in the seedling


X Hydathode (Hd) in the cotyledons








Table 3.
Promoter utility


Trait Area:
Nutrients


Sub-trait Area:
Nitrogen


Utility:
Among other uses this promoter sequence could be useful to modulate



tolerance to high nitrogen.







Notes: 1). There are 2 knock-out alleles in the Ceres population and 4 in the Salk population.


One of the knock-out alleles has a yellow-green viable phenotype.








Construct:
  PT0675


Promoter candidate I.D:
  15295952


cDNA I.D:
24418776 (OCKHAM3-CD)


Lines expressing:
PT0675-01, -02









(A) Predicted promoter sequence (1000 bp).










5′ CCAGTCGA▾TTGGCCCGAT▾CGGCC NNNNNNNNNNNNNN GGCCTGCA▾GGGCCAGTGCA▾CTGG 3′
(SEQ ID NO: 2)



 


>204.PT0675 predicted
(SEQ ID NO: 70)


ttgtttaacacctcaaacctgttaagactaatcacaatgttcgaagataatgccatttctatatatatttagtatagc


 


atcacacatgcgttctgtgttgcaaagtttactctagagttatcactgagtcatgactcatgatgaccattattatag


 


tattagtacttttaagttttaggtcgagaatatgaagctaatacatgcatgtaatgatgtaaatatgcctaccttaaa


 


aaatatcgaattattcagaaacaatgactcgatatccgtaagaaaccgccagctcctgctgaattgcatgaacctatc


 


ttaatattctttcgccacgaactcttcccttttgtctccttcttataactctacacatcatcatttcttttccactaa


 


ataacttacaatacgtatacctttttcttttttgtcaatttaaatcaacactaagatatactttaaatacgaatcatt


 


taaatgaatataatgtactaattgtttcagattttatttcctgtttaaaaatatactcatgaactaaaactaattaat


 


aaaatgtggataaattaaagccttttaacaaaaaaaaaatgtggataaattaatatcaatatgtttcctttttatttt


 


attttatctatttcaaaaaaataagttattcaatacatatgttgatattttgactatttttaatcataatttaaatca


 


attgttgtgttcttaagcaaaatatctaaaaacgaatataaccacgtccaccatagaagcactgcaattttagcattc


 


taaaacatccttgatatttttttgtcaacgtcttattatcttttatctcaaaccatgtatatggatgtatccactaac


 


gcatatatatagagacaattaggcatctatcattttatcccacacttatctcttcctatctctctctcattcaaaccc


 


aaataggaaacaaatacacaaaagtataataaaaagtctttctctcatctttcgccacgtagac






(B) Sequence verification and confirmation.









(SEQ ID NO: 71)









>204.PT0675 experimental



ttgtttaacacctcaaacctgttaagactaatcacaatgttcgaagataa


 


tgccatttctatatatatttagtatagcatcacacatgcgttctgtgttg


 


caaagtttactctagagttatcactgagtcatgactcatgatgaccatta


 


ttatagtattagtacttttaagttttaggtcgagaatgtgaagctaatac


 


atgcatgtaatgatgtaaatatgcctaccttaaaaaatatcgaattattc


 


agaaacaatgactcgatatccgtaagaaaccgccagctcctgctgaattg


 


catgaacctatcttaatattctttcgccacgaactcttcccttttgtctc


 


cttcttataactctacacatcatcatttcttttccactaaataacttaca


 


atacgtatacctttttcttttttgtcaatttaaatcaacactaagatata


 


ctttaaatacgaatcatttaaatgaatataatgtactaattgtttcagat


 


tttatttcctgtttaaaaatatactcatgaactaaaactaattaataaaa


 


tgtggataaattaaagccttttaacaaaaaaaaaatgtggataaattaat


 


atcaatatgtttcctttttattttattttatctatttcaaaaaaataagt


 


tattcaatacatatgttgatattttgactatttttaatcataatttaaat


 


caattgttgtgttcttaagcaaaatatctaaaaacgaatataaccacgtc


 


caccatagaagcactgcaattttagcattctaaaacatccttgatatttt


 


tttgtcaacgtcttattatcttttatctcagaccatgtatatggatgtat


 


ccactaacgcatatatatagagacaattaggcatctatcattttatccca


 


cacttatctcttcctatctctctctcattcaaacccaaataggaaacaaa


 


tacacaaaagtataataaaaagtctttctctcatctttcgccacgtagac


















Sequence (bp)
Mismatch
Predicted/Experimental







188
SNP
a/g


830
SNP
a/g







Sequence Q.C. notes:









(C) Predicted vs. Experimental sequence alignment.













Score = 1911 bits (994), Expect = 0.0


Identities = 998/1000 (99%)


Strand = Plus/Plus


Query = Predicted (SEQ ID NO: 70)


Subject = Experimental (SEQ ID NO: 71)


 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 

























Promoter Expression Report #205















Promoter Tested In: Arabidopsis thaliana, Wassilewskija (WS) ecotype


Spatial expression summary:








Silique
L funiculus H ovule


Ovule
  Post-fertilization: L funiculus H outer integument


Hypocotyl
  L epidermis


Cotyledon
  H epidermis H petiole


Rosette Leaf
  H epidermis H petiole


Primary Root
H endodermis







Observed expression pattern:


T1 mature: GFP expression highly specific to second cell layer of the outer integument in


developing seed. Also expressed at ovule connective site of funiculus. No expression


observed in pre-fertilized ovules.


T2 seedling: GFP exhibits expression in a highly polar fashion in cotyledons and rosette


leaves. GFP is expressed proximal-distal on the abaxial surface of the petioles of


cotyledons and rosette leaves with respect to the shoot apical meristem. Low GFP


expression observed on the adaxial surface of petioles of cotyledons and rosette


leaves. GFP expression in epidermal cells of hypocotyl at the root transition zone


decreases toward apex. Highly specific expression of GFP in endodermis cells of


the root.








Expected expression pattern:
   Shade Induced


Selection Criteria:
   Ceres expression data


Gene:
    Acyl CoA reductase, putative







GenBank: NM_122155 Arabidopsis thaliana acyl CoA reductase, putative/male-sterility protein,


putative (At5g22500) mRNA, complete cds gi|30688503|ref|NM_22155.2|[30688503]








Source Promoter Organism:
   Arabidopsis thaliana, Columbia ecotype


Vector:
   pNewbin4-HAP1-GFP


Marker Type:
  GFP-ER







Generation Screened:  XT1 Mature XT2 Seedling ↑T2 Mature ↑T3 Seedling


Inductions completed.
















Events Screened/



Treatment:
Age:
Gen:
Time points:
Response
Response:


1. Far red
7 days
T2
 1 Hr
2/0
No


Far Red730 = 525 μW/cm2


24 Hr
2/0
No







Inducible expression summary:










Treatment:
Time point induced:
Organs induced:
Tissues induced:








1. Far red
No differences observed. Images not shown.








T1 Mature Plant Expression
Organs/Tissues screened










Events Screened:
n = 3
Events Expressing:
n = 3








GFP Expression Detected



↑ Flower
↑pedicel ↑receptacle ↑nectary ↑sepal ↑petal ↑filament ↑anther ↑pollen



↑carpel ↑style ↑papillae ↑vascular ↑epidermis ↑stomata ↑trichome



↑silique


X Silique
↑stigma ↑style ↑carpel ↑septum ↑placentae L funiculus ↑transmitting tissue



↑vascular ↑epidermis ↑stomata ↑abscission zone H ovule


 X Ovule
Pre-fertilization: ↑primordia ↑inner integument ↑outer integument



↑funiculus ↑embryo sac ↑chalaza ↑micropyle ↑gametophyte



Post-fertilization: ↑zygote ↑suspensor ↑ embryo sack L funiculus ↑inner



integument H outer integument ↑endothelium ↑seed coat ↑primordia



↑chalaza ↑micropyle ↑early endosperm ↑mature endosperm ↑embryo


  ↑ Embryo
↑suspensor ↑preglobular ↑globular ↑heart ↑torpedo ↑late ↑mature



↑provascular ↑hypophysis ↑radicle ↑cotyledons ↑hypocotyl


↑ Stem
↑epidermis ↑cortex ↑vascular ↑xylem ↑phloem ↑pith ↑stomata ↑trichome


↑ Leaf
↑petiole ↑mesophyll ↑vascular ↑epidermis ↑trichome ↑primordia ↑stomata



↑stipule ↑margin


↑ Shoot apical meristem
↑shoot apical meristem ↑flower primordium







X Funiculus (Fn) in developing seed and placenta


X Outer integument cell layer 1 (Oi)1 in developing seed


X Outer integument cell layer 2 (Oi)2 in developing seed


X Placenta (Pl) in the placenta








T2 Seedling Expression
Tissues Screened








Events Screened: n = 2
Events Expressing: n = 2







Seedlings expressing/Seedlings screened


Event-01: 2(6)


Event-02: 2(6)


GFP Expression Detected








X Hypocotyl
L epidermis ↑cortex ↑vascular ↑xylem ↑phloem ↑stomata


X Cotyledon
↑ mesophyll ↑vascular H epidermis ↑margin H petiole ↑stomata



↑hydathode


X Rosette Leaf
↑ mesophyll ↑vascular H epidermis ↑trichome H petiole



↑primordia ↑stomata ↑stipule ↑margin ↑hydathode


X Primary Root
↑epidermis ↑trichoblast ↑atrichoblast ↑cortex H endodermis



↑vascular ↑xylem ↑phloem ↑pericycle ↑quiescent



↑columella ↑root cap ↑root hairs


↑ Lateral root
↑epidermis ↑trichoblast ↑atrichoblast ↑cortex ↑endodermis



↑initials ↑flanking cells ↑vascular ↑lateral root cap


↑ Shoot apical meristem
↑shoot apical meristem







X Abaxial (Ab) in the rosette leaf


X Adaxial (Ad) in the rosette leaf


X Cotyledon (Co) in the rosette leaf


X Endodermis (Eo) in the seedling


X Hypocotyl (Hy) in the seedling


X Petiole (Pt) in the rosette leaf


X Rosette leaf (Rl) in the rosette leaf


X Root (Rt) in the seedling








Promoter utility



Trait Area:
PG&D, nutrients


Sub-trait Area:
Nitrogen use efficiency, seed size


Utility:
Among other uses this promoter sequence could be useful to modulate







seed growth and development, seed dormancy and germination. Also, useful


for enhancement of leaf and root growth, resulting in increased source capacity


and water and nutrient loading. Useful in procedures and technologies aimed


at improving source-sink relationships and seed filling and yield.








Construct:
  PT0676


Promoter candidate I.D:
  15295958


cDNA I.D:
23658955


Lines expressing:
PT0676-01, -02; Apr. 12, 2004









(A) Predicted promoter sequence (1000 bp).










5′ CCAGTCGA▾TTGGCCCGAT▾CGGCC NNNNNNNNNNNNNN GGCCTGCA▾GGGCCAGTGCA▾CTGG 3′
(SEQ ID NO: 2)



 


>205.PT0676 predicted
(SEQ ID NO: 72)


aagatagtacagtttcagtgttttgagaaaaaaagctgaactaaaactaaaatgtttaaggacacaatatttagtttc


 


aattagataattcaacagtttgaacaattttttttttttttttttgaagtcatttatttatacaatgttttaaaacgc


 


attaagcatttaggcagccgacaaacgcctattgtctaactgtaaataggcgcttccacttaggttcatattgcatat


 


ttactatatgtgtatagtgacaaaaaccaatatttctcttattttggatgaaggtatagtagttgttaaatgttcaat


 


ataattaagcattaatgacaaataaaataaaattaatttagttgataaaaagataatcttataaaaagatcgatgaat


 


agatataatggtttactgaattctatagctcttaccttgcacgactatgtcccaaggagaggaagtaccttaactata


 


attctgaacataattttgtctatcttggtgagtattatatgacctaaaccctttaataagaaaaagtataatactggc


 


gtaacgtaataaattaacacaatcataagttgttgacaagcaaaaaaacatacataatttgtttaatgagatatatta


 


gttatagttcttatgtcaaagtacaattatgcctaccaaaattaattaatgatttcaacaggaagtctgagatgatgg


 


gccgacgtgtagttacgtttcttgaattgtgagagatggtatttattatactgaagaaaacattatttactaaataaa


 


ttttcatttcacatcttctgtaatcaatgcgggtagatgaagaagttgttaatacgatggccaaccatatggatctct


 


tttttggcgtttctatatatagtaacctcgactccaaaggcattacgtgactcaataaaatcaagtcttttgtttcct


 


tttatccaaaaaaaaaaaaaagtcttgtgtttctcttaggttggttgagaatcatttcatttca






(B) Sequence verification and confirmation.









(SEQ ID NO: 73)









>205.PT0676 experimental



aagatagtacagtttcagtgttttgagaaaaaaagctgaactaaaactaa


 


aatgtttaaggacacaatatttagtttcaattagataattcaacagtttg


 


aacaattttttttttttttttttgaagtcatttatttatacaatgtttta


 


aaacgcattaagcatttaggcagccgacaaacgcctattgtctaactgta


 


aataggcgcttccacttaggttcatattgcatatttactatatgtgtata


 


gtgacaaaaaccaatatttctcttattttggatgaaggtatagtagttgt


 


taaatgttcaatataattaagcattaatgacaaataaaataaaattaatt


 


tagttgataaaaagataatcttataaaaagatcgatgaatagatataatg


 


gtttactgaattctatagctcttaccttgcacgactatgtcccaaggaga


 


ggaagtaccttaactataattctgaacataattttgtctatcttggtgag


 


tattatatgacctaaaccctttaataagaaaaagtataatactggcgtaa


 


cgtaataaattaacacaatcataagttgttgacaagcaaaaaaacataca


 


taatttgtttaatgagatatattagttatagttcttatgtcaaagtacaa


 


ttatgcctaccaaaattaattaatgatttcaacaggaagtctgagatgat


 


gggccgacgtgtagttacgtttcttgaattgtgagagatggtatttatta


 


tactgaagaaaacattatttactaaataaattttcatttcacatcttctg


 


taatcaatgcgggtagatgaagaagttgttaatacgatggccaaccatat


 


ggatctcttttttggcgtttctatatatagtaacctcgactccaaaggca


 


ttacgtgactcaataaaatcaagtcttttgtttccttttatccaaaaaaa


 


aaaaaaagtcttgtgtttctcttaggttggttgagaatcatttcatttca






(C) Predicted vs. Experimental sequence alignment.













Sequence (bp)
Mismatch
Predicted/Experimental
















1–1000








Sequence Q.C. notes:





















(Query: SEQ ID NO: 72)


(Subject: SEQ ID NO: 73)


Score = 1917 bits (997), Expect = 0.0


Identities = 999/1000 (99%)


Strand = Plus/Plus


 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 



























Promoter Expression Report #206


Promoter Tested In: Arabidopsis thaliana, Wassilewskija (WS) ecotype


Spatial expression summary:








Hypocotyl
H vascular


Cotyledon
L epidermis


Rosette Leaf
L vascular







Primary Root  H vascular H root cap


Observed expression pattern:


T1 mature: No expression observed.


T2 seedling: High GFP expression in vasculature of root and hypocotyl decreasing toward


shoot and root apices. High GFP expression in cells of the root cap. Low epidermal


expression in cotyledons.








Expected expression pattern:
Shade Inducible


Selection Criteria:
   Microarray







Gene: Auxin-responsive protein/indoleacetic acid-induced protein 1 (IAA1)


GenBank: NM_117536 Arabidopsis thaliana auxin-responsive protein/indoleacetic


acid-induced protein 1 (IAA1) (At4g14560) mRNA, complete


cds gi|30682899|ref| NM_117536.








Source Promoter Organism:
Arabidopsis thaliana, Columbia (Col) ecotype


Vector:
pNewbin4-HAP1-GFP


Marker Type:
GFP-ER







Generation Screened:  XT1 Mature XT2 Seedling ↑T2 Mature ↑T3 Seedling


Inductions completed.
















Events Screened/



Treatment:
Age:
Gen:
Time points:
Response
Response:


1. Far red
7 days
T2
 1 Hr
5/2
Yes


Far Red730 = 525 μW/cm2


24 Hr
5/2
Yes







Inducible expression summary:










Treatment:
Time point induced:
Organs induced:
Tissues induced:


1. Far red
1 Hr, 24 Hr
Cotyledon
Vascualture, Epidermis




Rosette Leaf
Vascualture, Epidermis




Primary Root
Vascualture, Root Cap




Lateral root
Lateral root cap







T1 Mature Plant Expression   Organs/Tissues screened


Events Screened:   n = 3       Events Expressing:   n = 0


X No GFP Expression Detected


T2 Seedling Expression    Tissues Screened


Events Screened: n = 2      Events Expressing: n = 2


Seedlings expressing/Seedlings screened


Event-01: 5(6)


Event-04: 4(6)


GFP Expression Detected








X Hypocotyl
↑epidermis ↑cortex H vascular ↑xylem ↑phloem ↑stomata


X Cotyledon
↑mesophyll ↑vascular L epidermis ↑margin ↑stomata



↑hydathode


X Rosette Leaf
↑mesophyll L vascular ↑epidermis ↑trichome ↑petiole



↑primordia ↑stomata ↑stipule ↑margin ↑hydathode


X Primary Root
↑epidermis ↑trichoblast ↑atrichoblast ↑cortex ↑endodermis



H vascular ↑xylem ↑phloem ↑pericycle ↑quiescent



↑columella H root cap ↑root hairs


↑ Lateral root
↑epidermis ↑trichoblast ↑atrichoblast ↑cortex ↑endodermis



↑initials ↑flanking cells ↑vascular ↑lateral root cap


↑ Shoot apical meristem
↑shoot apical meristem







X Epidermis (Ep) in the cotyledons


X Hypocotyl (Hy) in the root


X Root cap (Rc) in the root


X Vasculature (Vs) in the seedling, hypocotyl, and root


Promoter utility








Trait Area:
Nutrients


Sub-trait Area:
Nitrogen transport


Utility:
Among other uses this promoter sequence could be useful to modulate



nitrogen transport.








Construct:
PT0680


Promoter candidate I.D:
15295973


cDNA I.D:
23535379 (13617391)


Lines expressing:
PT0680-01, -04









(A) Predicted promoter sequence (1000 bp).










5′ CCAGTCGA▾TTGGCCCGAT▾CGGCC NNNNNNNNNNNNNN GGCCTGCA▾GGGCCAGTGCA▾CTGG 3′
(SEQ ID NO: 2)



 


>206.PT0680 predicted
(SEQ ID NO: 74)


aaaatgttatttgagacagcatatcacatggccttaccatacttcctgcatccattattccattaagaacactcttca


 


ccctcatccacatgcatctccctccccaatttatttactattgatcataattgtacaaacctatacttacaatttata


 


tatgtgtctacgagaaaataaataatattttacagtgttttgtctattattttgttctatagtttcttgcaaacaaaa


 


cattacttttcacgcaaaaactgtcgaaatatttataaaaggaaattgttaattcttcgatacaaattgaccattaat


 


atttgatcatctattctagacatctactctaccatataccaaacctttacacaaaaatgaaatattttcatgaaaact


 


accccacaactggggtgatcgaaaaagcttgatctatatgatcaacatgtccaacactagtttcattttttctactat


 


gatatccgatgatccaatctgaactatacaaaatgtatctagatattttcttgaatcaatccgaataacgaatagttg


 


caaaacataaacctagcgtgatcgtgtggtagaaggacgaaggtcgagaagttctcttactcttatgattttctcttt


 


actcatttgaccgtaagagaaagaaacggctaggatctcgcgtacgcaactggcggagacaaatcaggaccgttgaaa


 


ataagaaagaagccgcgtccaaaatctttgtgtcccacctttgtccccttgcctctaacttgcctcctcatgctcccc


 


gacaacgtcataattcatatctctctctctctctcgttaaccctaatttcaaagcatctttccttatataaatctctc


 


tctctccctcaccattacacaacacacacaagcattttcaaggatatcaaatcacaatcccaagaagagcaataacaa


 


gagaagaagaagtagttcaagaattaaggaagagagcttctccgttaaagtatagtgagagaat






(B) Sequence verification and confirmation.









(SEQ ID NO: 75)









>206.PT0680 experimental



aaaatgttatttgagacagcatatcacatggccttaccatacttcctgca


 


tccattattccattaagaacactcttcaccctcatccacatgcatctccc


 


tccccaatttatttactattgatcataattgtacaagcctatacttacaa


 


tttatatatgtgtctacgagaaaataaataatattttacagtgttttgtc


 


tattattttgttctatagcttcttgcaaacaagacattacttttcacgca


 


aaaactgtcgaaatatttataaaaggaaattgttaattcttcgatacaaa


 


ttgaccattaatatttgatcatctattctagacatctactctaccatata


 


ccaaacctttacacaaaaatgaaatattttcatgaaaactaccccacaac


 


tggggtgatcgaaaaagcttgatctatatgatcaacatgtccaacactag


 


tttcattttttctactatgatatccgatgatccaatctgaactatacaaa


 


atgtatctagatattttcttgaatcaatccgaataacgaatagttgcaaa


 


acataaacctagcgtgatcgtgtggtagaaggacgaaggtcgagaagttc


 


tcttactcttatgatgttctctttactcatttgaccgtaagagaaagaaa


 


cggctaggatctcgcgtacgcaactggcggagacaaatcaggaccgttga


 


aaataagaaagaagccgcgtccaaaatctttgtgtcccacctttgtcccc


 


ttgcctctaacttgcctcctcatgctccccgacaacgtcataattcatat


 


ctctctctctctctcgttaaccctaatttcaaagcatctttccttatata


 


aatctctctctctccctcaccattacacaacacacacaagcattttcaag


 


gatatcaaatcacaatcccaagaagagcaataacaagagaagaagaagta


 


gttcaagaattaaggaagagagcttctccgttaaagtatagtgagagaat


















Sequence (bp)
Mismatch
Predicted/Experimental







137
SNP
a/g


219
SNP
t/c


233
SNP
a/g


616
SNP
t/g







Sequence Q.C. notes:









(C) Predicted vs. Experimental sequence alignment.













Query = Predicted (SEQ ID NO: 74)


Subject = Experimental (SEQ ID NO: 75)


Score = 1900 bits (988), Expect = 0.0


Identities = 996/1000 (99%)


Strand = Plus/Plus


 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 



























Promoter Expression Report #208


Promoter Tested In: Arabidopsis thaliana, Wassilewskija (WS) ecotype


Spatial expression summary:








Flower
  H pollen


Ovule
  Pre-fertilization: H gametophyte


Embryo
H torpedo H late H mature H root meristem H shoot meristem


Cotyledon
  H epidermis


Rosette Leaf
  H epidermis H trichome H petiole


Primary Root
H epidermis H cortex H quiescent L root cap


Lateral root
H epidermis







Observed expression pattern:


T1 mature: GFP expressed in female gametophyte of developing ovules, pollen and in shoot and root apical


meristems in torpedo through mature stage embryos. GFP also detected in suspensor cells of developing


embryos. In mature embryos, GFP expression in the quiescent center can be clearly distinguished from


root cap.


T2 Seedling: Predominantly expressed in the epidermis of petioles and rosette leaves. In the lower root, GFP


expression in the epidermis appears to coincide with position of lateral root formation. At the root tip, GFP


expression in the quiescent center can be clearly distinguished from root cap.








Expected expression pattern:
Shade inducible


Selection Criteria:
Microarray







Gene: FAD-binding domain-containing protein/cytokinin oxidase family protein


GenBank: NM_106199 Arabidopsis thaliana FAD-binding domain-containing protein/cytokinin


oxidase family protein (At1g75450) mRNA, complete cds gi








Source Promoter Organism:
Arabidopsis thaliana, Columbia (Col) ecotype


Vector:
pNewbin4-HAP1-GFP


Marker Type:
GFP-ER







Generation Screened:  XT1 Mature XT2 Seedling ↑T2 Mature ↑T3 Seedling


Inductions completed.
















Events Screened/



Treatment:
Age:
Gen:
Time points:
Response
Response:


1. Far red
7 days
T2
 1 Hr
5/1
Yes


Far Red730 = 525 μW/cm2


24 Hr
5/3
Yes







Inducible expression summary:










Treatment:
Time point induced:
Organs induced:
Tissues induced:


1. Far red
 1 Hr
Rosette leaf,
Epidermis




Petiole
Epidermis



24 Hr
Cotyledons
Epidermis




Rosette leaf
Epidermis




Petiole
Epidermis








T1 Mature Plant Expression
Organs/Tissues screened


Events Screened:    n = 6
   Events Expressing:   n = 2







 GFP Expression Detected








X Flower
↑pedicel ↑receptacle ↑nectary ↑sepal ↑petal ↑filament ↑anther H pollen



↑carpel ↑style ↑papillae ↑vascular ↑epidermis ↑stomata ↑trichome



↑silique


↑ Silique
↑stigma ↑style ↑carpel ↑septum ↑placentae ↑transmitting tissue ↑vascular



↑epidermis ↑stomata ↑abscission zone ↑ovule


X Ovule
Pre-fertilization: ↑primordia ↑inner integument ↑outer integument ↑embryo



sac ↑funiculus ↑chalaza ↑micropyle H gametophyte


X Embryo
Post-fertilization: ↑zygote ↑suspensor ↑embryo sack ↑funiculus ↑inner



integument ↑outer integument ↑endothelium ↑seed coat ↑primordia ↑chalaza



↑micropyle ↑early endosperm ↑mature endosperm ↑embryo



↑suspensor ↑preglobular ↑globular ↑heart H torpedo H late H mature



↑provascular ↑hypophysis ↑radicle ↑cotyledons ↑hypocotyl



H root meristem H shoot meristem


↑ Stem
↑epidermis ↑cortex ↑vascular ↑xylem ↑phloem ↑pith ↑stomata ↑trichome


↑ Leaf
↑petiole ↑mesophyll ↑vascular ↑epidermis ↑trichome ↑primordia ↑stomata



↑stipule ↑margin


↑ Shoot apical meristem
↑shoot apical meristem ↑flower primordium







X Female gametophyte (Fmg) in the ovule


X Pollen (Po) in the ovule


X Quiescent center (Qc) in the embryo


X Shoot apical meristem (SAM) in the embryo


X Suspensor (Su) in the ovule


X Root apical meristem (RAM) in the embryo


X Root cap (Rc) in the embryo








T2 Seedling Expression
Tissues Screened


Events Screened:   n = 2
   Events Expressing: n = 2







Seedlings expressing/Seedlings screened


Event-01: 4/6


Event-03: 2/6


GFP Expression Detected








↑ Hypocotyl
↑epidermis ↑cortex ↑vascular ↑xylem ↑phloem ↑stomata


X Cotyledon
↑mesophyll ↑vascular H epidermis ↑margin ↑stomata ↑hydathode


X Rosette Leaf
↑mesophyll ↑vascular H epidermis H trichome H petiole ↑primordia



↑stomata ↑stipule ↑margin ↑hydathode


X Primary Root
H epidermis ↑trichoblast ↑atrichoblast H cortex ↑endodermis ↑vascular



↑xylem ↑phloem ↑pericycle H quiescent ↑columella L root cap ↑root hairs


X Lateral root
H epidermis ↑trichoblast ↑atrichoblast ↑cortex ↑endodermis ↑initials



↑flanking cells ↑vascular ↑lateral root cap


↑ Shoot apical meristem
↑shoot apical meristem







X Cortex (Cr) in the root


X Epidermis (Ep) in the cotyledon, rosette leaf, and the root


X Lateral root (Lr) in the root


X Petiole (Pt) in the rosette leaf


X Quiescent center (Qc) in the root


X Rosette leaf (Rl)


X Root cap (Rc) in the root


Promoter utility








Trait Area:
PG&D, water use efficiency, source


Sub-trait Area:
Drought, heat, yield, shade avoidance, growing rate


Utility:
Among other uses this promoter sequence could be useful to modulate



seed size, drought tolerance, yield, and growth rate. Useful to drive genes



to repress shade avoidance responses - reduction of petiole elongation and



early flowering.


Construct:
PT0682


Promoter candidate I.D:
15295985


cDNA I.D:
23530913


Lines expressing:
PT0682-01, PT0682-03









(A) Predicted promoter sequence (1000 bp).










5′ CCAGTCGA▾TTGGCCCGAT▾CGGCC NNNNNNNNNNNNNN GGCCTGCA▾GGGCCAGTGCA▾CTGG 3′
(SEQ ID NO: 2)



 


>208.PT0682 predicted
(SEQ ID NO: 76)


cactacacacgtgtgacctcatcctctcccacgtgaatatccacgtggcgttcttccgttccgtttctcccatccctc


 


ccatgcctctccccatgactctatttatcccaatcctctcttcctttcattaatttatcagttaaaattcctcttttt


 


tcctagtagtatttggagttttcatatcaaaaagtttagactaaccctaaaaacattgatagaaaaacttatcatttt


 


aaacgttcttggggaccaatcaaaatggttaattgtctagtgcctgttcttgattcttcagacatggttgcaaaagtc


 


catagtcaaatcaaggttatatgtagcttcaacactgataacacgtttattaacaaaaccatatcaaaatggttgttt


 


tttgcattttcagtcttgacgtatacactgccatttttgaattagtcaaatcgttacgtagttggtctacgatgtctc


 


gctgaaacaaatacatacgtgtgtatatacactatgcaagtagtatagttaacatcataattgaccctaaggaaaaaa


 


gttaatgtaaacagtgacacgtagatatcacacggttcttttttggtttttgttaaagatgaacttgttaataaagaa


 


tatgacgtgatcttctccggtacaactctttgtcctataaatagagaactcttgtcttcatattctcgacacacacat


 


ataaacgcacaaactcgttaaatttgtacgaatataattttttttaaaacactcgttataatatattaaagtttcacc


 


caaaccgaaaaaagagagaatctgtgcatgttgctcagaaaatcttcaaagcgtaatctgggcttacgttagctctca


 


cgaacccccaaggatcttctatatatgttttttcatttccccataaaatctttcattatctaaaaaatattattatcg


 


tatcttttttcttctatatattcttcctcctcaatcttgattcttgtttcttgagtattctttg






(B) Sequence verification and confirmation.









(SEQ ID NO: 77)









>208.PT0682 experimental



cactaaacacgtgtgacctcatcctctcccacgtgaatatccacgtggcg


 


ttcttccgttccgtttctcccatccctcccatgcctctccccatgactct


 


atttatcccaatcctctcttcctttcattaatttatcagttaaaattcct


 


cttttttcctagtagtatttggagttttcatatcaaaaagtttagactaa


 


ccctaaaaacattgatagaaaaacttatcattttaaacgttcttggggac


 


caatcaaaatggttaattgtctagtgcctgttcttgattcttcagacatg


 


gttgcaaaagtccatagtcaaatcaaggttatatgtagcttcaacactga


 


taacacgtttattaacaaaccatatcaaaatggttgttttttgcattttc


 


agtcttgacgtatacactgccatttttgaattagtcaaatcgttacgtag


 


ttggtctacgatgtctcgctgaaacaaatacatacgtgtgtatatacact


 


atgcaagtagtatagttaacatcataattgaccctaaggaaaaagttaat


 


gtaaacagtgacacgtagatatcacacggttcttttttggtttttgttaa


 


agatgaacttgttaataaagaatatgacgtgatcttctccggtacaactc


 


tttgtcctataaatagagaactcttgtcttcatattctcgacacacacat


 


ataaacgcacaaactcgttaaatttgtacgaatataattttttttaaaac


 


actcgttataatatattaaagtttcacccaaaccgaaaaaagagagaatc


 


tgtgcatgttgctcagaaaatcttcaaagcgtaatctgggcttacgttag


 


ctctcacgaacccccaaggatcttctatatatgttttttcatttccccat


 


aaaatctttcattatctaaaaaatattattatcgtatcttttttcttcta


 


tatattcttcctcctcaatcttgattcttgtttcttgagtattctttg


















Sequence (bp)
Mismatch
Predicted/Experimental

















6
SNP
c/a


370
SNP
a/—


547
SNP
a/—







Sequence Q.C. notes:









(C) Predicted vs. Experimental sequence alignment.













Query = Predicted (SEQ ID NO: 76)


Subject = Experimental (SEQ ID NO: 77)


Score = 1886 bits (981), Expect = 0.0


Identities = 997/1000 (99%), Gaps = 2/1000 (0%)


Strand = Plus/Plus


 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 



























Promoter Expression Report #209


Promoter Tested In: Arabidopsis thaliana, Wassilewskija (WS) ecotype


Spatial expression summary:








Primary Root
H epidermis H cortex H trichoblast H atrichoblast



H root hairs







Observed expression pattern:


T1 mature: No expression observed.


T2 seedling: Root specific GFP expression. GFP expressed in root hair and non-root hair


epidermal cells and cortex.








Expected expression pattern:
Shade induced


Selection Criteria:
Microarray


Gene:
   Cytochrome P450, CYP96A5







GenBank: NM_127760 Arabidopsis thaliana cytochrome P450, putative


(At2g21910) mRNA, complete cds gi|18399829|ref|NM_127760.1|[18399829]








Source Promoter Organism:
Arabidopsis thaliana, Columbia (Col) ecotype


Vector:
pNewbin4-HAP1-GFP


Marker Type:
GFP-ER







Generation Screened:  XT1 Mature XT2 Seedling ↑T2 Mature ↑T3 Seedling


Inductions completed.
















Events Screened/



Treatment:
Age:
Gen:
Time points:
Response
Response:


1. Far red
7 days
T2
 1 Hr
5/1
Yes


Far Red730 = 525 μW/cm2


24 Hr
5/5
Yes







Inducible expression summary:










Treatment:
Time point induced:
Organs induced:
Tissues induced:


1. Far red
 1 Hr
Cotyledons
Epidermis



24 Hr
Cotyledons
Epidermis




Rosette leaf
Epidermis




Petioles
Epidermis








T1 Mature Plant Expression
Organs/Tissues screened


Events Screened:   n = 3
   Events Expressing:   n = 0


X No GFP Expression Detected


T2 Seedling Expression
Tissues Screened


Events Screened: n = 2
   Events Expressing: n = 2







Seedlings expressing/Seedlings screened


Event-01: 5/6


Event-02: 5/6


GFP Expression Detected








↑ Hypocotyl
↑epidermis ↑cortex ↑vascular ↑xylem ↑phloem ↑stomata


↑ Cotyledon
↑mesophyll ↑vascular ↑epidermis ↑margin ↑stomata



↑hydathode


↑ Rosette Leaf
↑mesophyll ↑vascular ↑epidermis ↑trichome ↑petiole



↑primordia ↑stomata ↑stipule ↑margin ↑hydathode


X Primary Root
H epidermis H trichoblast H atrichoblast H cortex ↑endodermis



↑vascular ↑xylem ↑phloem ↑pericycle ↑quiescent



↑columella ↑root cap H root hairs


↑ Lateral root
↑epidermis ↑trichoblast ↑atrichoblast ↑cortex ↑endodermis



↑initials ↑flanking cells ↑vascular ↑lateral root cap


↑ Shoot apical meristem
↑shoot apical meristem







X Cortex (Cr) in the root


X Epidermis (Ep) in the root


X Root hair (Rh) in the root


Promoter utility








Trait Area:
Nutrients, PG&D


Sub-trait Area:
Nitrogen use efficiency, shade avoidance, plant size







Utility: Among other uses this promoter sequence could be useful to modulate nitrogen use


efficiency, plant size, and shade avoidance. Root expression can be used to modify root


architecture and tissue specific location of proteins. Expression in root cortex can be used to


improve nitrogen transport to the phloem and xylem. Shade expression could be used to


express negative regulators of shade response, e.g., inhibition of petiole elongation.








Construct:
PT0683


Promoter candidate I.D:
15295991


cDNA I.D:
23499869


Lines expressing:
PT0683-01, PT0683-02









(A) Predicted promoter sequence (1000 bp).










5′ CCAGTCGA▾TTGGCCCGAT▾CGGCC NNNNNNNNNNNNNN GGCCTGCA▾GGGCCAGTGCA▾CTGG 3′
(SEQ ID NO: 2)



 


>209.PT0683 predicted
(SEQ ID NO: 78)


gattgaatgatgagtgtgcacccttgtattactaataaaaaatttagcaacagttataagctaacgtcatccatgagt


 


cattcattagattcactatttgcgttctcaaaaatcgaattgttaaaatttgagaagctctaatatacgagtcaatga


 


gatgtggcaaaagcatgtccttgaccataaaatttcgaggggtcaactcattagataaggacaagaatcaaccaattg


 


aaggcgtcttctataacaagtttctttattactaatattaaagtccaatggggtgagggggagaagaacttaaataaa


 


aggaaataattggtaagtgaataaaatctaaatacgatactagatgattgatttgtgctagtgcatggtattagatca


 


gatatgtgttactattcgaattcaaattggcatattccatgttgttgataagaaaattgtagaagtgtaaaagctgag


 


ttactatattcaaactagtggtttacataaagtgagacaacaactgtttcacaaaaatgactataaaatagtaagtag


 


tattaggtcaattgattttaaaattttaatcaaattcaaatttgtgatataatcaaatttgtttatagaaaatgttaa


 


gaaatcaattttggcagaactaattcagtgagaaacaatcatttacaaaaacaattttaacattatttaacagtaaga


 


tttgacatttaacccgttcgtgtgaacccatcatatctaacatggctctacccatgacgcctccatgccatggacaat


 


tttgacagatcagaagttctgaacgtggacgaggtaagaacaccatgatgatacgattggagttagttatgtcgccac


 


cgacatcactgccaatctcattaataaaagtggtactaaatctctaatctctattaactataaatataacaaagaacc


 


aaaagaaagtttcttatctctcttatctttcataatttccaagaaacacaaaccttttctacta






(B) Sequence verification and confirmation.









(SEQ ID NO: 79)









>209.PT0683 experimental



gattgaatgatgagtgtgcacccttgtattactaataaaaaatttagcaa


 


cagttataagctaacgtcatccatgagtcattcattagattcactatttg


 


cgttctcaaaaatcgaattgttaaaatttgagaagctctaatatacgagt


 


caatgagatgtggcaaaagcatgtccttgaccataaaatttcgaggggtc


 


aactcattagataaggacaagaatcaaccaattgaaggcgtcttctataa


 


caagtttctttattactaatattaaagtccaatggggtgagggggagaag


 


aacttaaataaaaggaaataattggtaagtgaataaaatctaaatacgat


 


actagatgattgatttgtgctagtgcatggtattagatcagatatgtgtt


 


actattcgaattcaaattggcatattccatgttgttgataagaaaattgt


 


agaagtgtaaaagctgagttactatattcaaactagtggtttacataaag


 


tgagacaacaactgtttcacaaaaatgactataaaatagtaagtagtatt


 


aggtcaattgattttaaaattttaatcaaattcaaatttgtgatataatc


 


aaatttgtttatagaaaatgttaagaaatcaattttggcagaactaattc


 


agtgagaaacaatcatttacaaaaacaattttaacattatttaacagtaa


 


gatttgacatttaacccgttcgtgtgaacccatcatatctaacatggctc


 


tacccatgacgcctccatgccatggacaattttgacagatcagaagttct


 


gaacgtggacgaggtaagaacaccatgatgatacgattggagttagttat


 


gtcgccaccgacatcactgccaatctcattaataaaagtggtactaaatc


 


tctaatctctattaactataaatataacaaagaaccaaaagaaagtttct


 


tatctctcttatctttcataatttccaagaaacacaaaccttttctacta


















Sequence (bp)
Mismatch
Predicted/Experimental







427
SNP
t/c







Sequence Q.C. notes:









(C) Predicted vs. Experimental sequence alignment.













Query = Predicted (SEQ ID NO: 78)


Subject = Experimental (SEQ ID NO: 79)


Score = 1917 bits (997), Expect = 0.0


Identities = 999/1000 (99%)


Strand = Plus/Plus


 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 



























Promoter Expression Report #233


Promoter Tested In: Arabidopsis thaliana, WS ecotype


Spatial expression summary:








Cotyledon
L epidermis







Observed expression pattern:


T1 mature: No expression observed.


T2 seedling: Weak epidermal expression in cotyledons.








Expected expression pattern:
Shade Induced


Selection Criteria:
Microarray data


Gene:
   expressed protein







GenBank: NM_124668 Arabidopsis thaliana expressed protein (At5g52900) mRNA,


complete cds gi|30696256|ref|NM_124668.2|[30696256]








Source Promoter Organism:
Arabidopsis thaliana WS


Vector:
pNewbin4-HAP1-GFP


Marker Type:
GFP-ER







Generation Screened:  XT1 Mature XT2 Seedling ↑T2 Mature ↑T3 Seedling


Inductions completed.
















Events Screened/



Treatment:
Age:
Gen:
Time points:
Response
Response:


1. Far red
7 days
T2
1 Hr
6/0
No


Far Red730 = 525 μW/cm2


4 Hr
6/0
No





24 Hr 
6/0
No







Inducible expression summary:










Treatment:
Time point induced:
Organs induced:
Tissues induced:








T1 Mature Plant Expression
Organs/Tissues screened


Events Screened:   n = 3
Events Expressing:   n = 0


X No GFP Expression Detected


T2 Seedling Expression
Tissues Screened


Events Screened: n = 3
Events Expressing: n = 2







Seedlings expressing/Seedlings screened


Event-01: 1/6


Event-03: 0/6


Event-06: 2/6


GFP Expression Detected








↑ Hypocotyl
↑epidermis ↑cortex ↑vascular ↑xylem ↑phloem ↑stomata


X Cotyledon
↑mesophyll ↑vascular L epidermis ↑margin ↑stomata



↑hydathode


↑ Rosette Leaf
↑mesophyll ↑vascular ↑epidermis ↑trichome ↑petiole



↑primordia ↑stomata ↑stipule ↑margin ↑hydathode


↑ Primary Root
↑epidermis ↑trichoblast ↑atrichoblast ↑cortex ↑endodermis



↑vascular ↑xylem ↑phloem ↑pericycle ↑quiescent



↑columella ↑root cap ↑root hairs


↑ Lateral root
↑epidermis ↑trichoblast ↑atrichoblast ↑cortex ↑endodermis



↑initials ↑flanking cells ↑vascular ↑lateral root cap


↑ Shoot apical meristem
↑Shoot apical meristem








Construct:
PT0687


Promoter candidate I.D:
15296009


cDNA I.D:
23457674


Lines expressing:
PT0687-01, -06









(A) Predicted promoter sequence (1000 bp).









5′ CCAGTCGA▾TTGGCCCGAT▾CGGCC



 


(nucletides 1–23 of SEQ ID NO: 2)


 








(SEQ ID NO: 56)









caacaaacattcccttggagatttgagagattcatatcattaaatgcact



 


tctcaatatacggagtattactaattaaaaccttatttcgagttctctca


 


aacgtaacccatgcaaaaatggccccagagataagactttgatgagtctc


 


cacgtcactttctgatttcggcttttgtcccctaatctttcgacaacatt


 


cgtctcgcaccccgacatttcccgggacctctgtctctccccctctcttt


 


ctcctctcctctcccatttctcaacttttttccttattcacgaaatagac


 


tttttttattttagttttcttttctcccatttgtaactcgtggtccttct


 


tcatttgtattaatgctctggaaattttcttcttaaaacgttatacagct


 


atttttgctttttcctatacatattcgtttcatagttgtgttttctttgt


 


ctatcaaaacaattagttccatgagatatgtgtcaatacttaacatgcat


 


cgtctttttctgatttgtggataactctctaaacaaattaaaataatcat


 


gctctaggagaggagataacgtcattcatatcatgatcttcctaattaaa


 


atataattatgttgccaccgggaatataattaaaataaccctatattcga


 


aaagaaaagagaaaacaaaaactaaaaaaaaaaaggaaaggagtgaaggc


 


aacagcacataatgagaggttagtatgggctcacaaactcttatgtttct


 


tttcttttcttttttccctttccaattattaatatctattgtttcttacc


 


aaactaaccacatatatatttatatattaccgttattaaattaaaataaa


 


attatgtgtatatgtccctctctatatataaacactgaaacatatgttcc


 


caattcaaaaaattgttttgtctcaaacaaatttctctgcacacactcaa


 


caacatatcccataacaaaaaaaagctattaaaaaaaaagagaagcagcc


 


(nucletides 38–60 of SEQ ID NO: 2)


 


GGCCTGCA▾GGGCCAGTGCA▾


 


CTGG 3′






(B) Sequence verification and confirmation.













Sequence (bp)
Mismatch
Predicted/Experimental















Sequence Q.C. notes:









(C) Predicted vs. Experimental sequence alignment.













Query = Predicted (SEQ ID NO: 56)


Subject = Experimental (SEQ ID NO: 56)


Score = 1923 bits (1000), Expect = 0.0


Identities = 1000/1000 (100%)


Strand = Plus/Plus


 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 








 















The invention being thus described, it will be apparent to one of ordinary skill in the art that various modifications of the materials and methods for practicing the invention can be made. Such modifications are to be considered within the scope of the invention as defined by the following claims.
Each of the references from the patent and periodical literature cited herein is hereby expressly incorporated in its entirety by such citation.

## Claims

1. An isolated nucleic acid molecule consisting of the nucleotide sequence set forth in SEQ ID NO: 56 which acts as a plant promoter.

2. A polynucleotide comprising the plant promoter according to claim 1 operatively linked to a heterologous sequence.

3. The polynucleotide according to claim 2 wherein the heterologous sequence encodes a detectable product.

4. A vector comprising the polynucleotide according to claim 2.

5. A host cell stably transformed with the polynucleotide according to claim 2.

6. A host cell stably transformed with the vector according to claim 4.

7. A transformed plant cell comprising a plant promoter consisting of the nucleotide sequence according to claim 1, operatively linked to a heterologous sequence.

8. The plant cell of claim 7, wherein the plant cell is a monocot plant cell.

9. The plant cell of claim 7, wherein the plant cell is a dicot plant cell.

10. A transgenic plant comprising a genome that includes a plant promoter consisting of the nucleotide sequence set forth in SEQ ID NO: 56, operatively linked to a heterologous sequence.

11. The transgenic plant of claim 10, wherein the plant is selected from the group consisting of canola, crambe, mustard, castor bean, sesame, cottonseed, linseed, maize, soybean, Arabidopsis, Phaseolus, peanut, alfalfa, wheat, rice, oat, sorghum, rapeseed, rye, tritordeum, millet, fescue, perennial, ryegrass, sugarcane, cranberry, papaya, banana, safflower, oil palms, flax, muskmelon, apple, cucumber, dendrobium, gladiolus, chrysanthemum, liliacea, cotton, eucalyptus, sunflower, Brassica campestris, Brassica napus, turfgrass, sugarbeet, coffee, dioscorea and a monocot plant.

12. A seed from the plant of claim 10, wherein said seed contains said plant promoter operatively linked to said heterologous sequence.

13. A method of producing a transformed plant cell, the method comprising introducing into a plant cell a plant promoter consisting of the nucleotide sequence set forth in SEQ ID NO: 56, whereby said plant promoter is operatively linked to a heterologous sequence in said transformed plant cell.

14. A method of producing a transgenic plant, the method comprising: introducing into a plant cell the plant promoter according to claim 1, whereby said plant promoter is operatively linked to a heterologous sequence in said transformed plant cell and cultivating the cell to generate a plant.

15. A DNA construct comprising the promoter DNA sequence set forth in SEQ ID NO: 56; a structural DNA sequence; and a 3′ non-translated region that functions in plants to cause the addition of polyadenylated nucleotides to the 3′ end of the RNA sequence; wherein the structural DNA sequence is operably linked to the promoter and the 3′ non-translated region, and the promoter DNA sequence is heterologous with respect to the structural DNA sequence.

16. A transgenic crop plant comprising the DNA construct of claim 15.

17. A method of expressing a structural DNA sequence in a plant, the method comprising: (1) providing a DNA construct comprising a promoter that is SEQ ID NO: 56; a structural DNA sequence; and a 3′ non-translated region that functions to cause the addition of polyadenylated nucleotides to the 3′ end of the RNA sequence; wherein the structural DNA sequence is operably linked to the promoter and the 3′ non-translated region, and the promoter is heterologous with respect to the structural DNA sequence; (2) introducing the DNA construct into a plant cell; and (3) regenerating the plant cell to produce a plant such that the structural DNA sequence is expressed in the plant.

18. A transformed plant comprising the plant promoter according to claim 1 operatively linked to a heterologous sequence, wherein said transformed plant having increased expression of said heterologous sequence when the transformed plant is grown under shade conditions compared to a wild-type plant of the same species cultivated under the same conditions.

19. A seed of the plant according to claim 18, wherein said seed contains the plant promoter of SEQ ID NO: 56 operatively linked to said heterologous sequence.

20. A method of producing a transformed plant having increased expression of a heterologous sequence when the transformed plant is grown under shade conditions compared to a wild-type plant of the same species cultivated under the same conditions, which comprises introducing the plant promoter according to claim 1 operatively linked to the heterologous sequence into a plant cell to increase expression of the heterologous sequence in said plant cell and regenerating a plant from said plant cell.