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.

1 . An isolated nucleic acid molecule capable of modulating transcription wherein the nucleic acid molecule shows at least 80% sequence identity to a sequence set forth in Table 1, or a complement thereof. 
     
     
         2 . The isolated nucleic acid molecule of  claim 1 , wherein said nucleic acid is capable of functioning as a promoter. 
     
     
         3 . The isolated nucleic acid molecule of  claim 2 , wherein said nucleic acid comprises a reduced promoter nucleotide sequence having a sequence consisting of a SEQ ID NO. in Table 1 having at least one of the corresponding optional promoter fragments identified in Table 3 deleted therefrom. 
     
     
         4 . The isolated nucleic acid molecule of  claim 2 , wherein said nucleic acid comprises a reduced promoter nucleotide sequence having a sequence consisting of a SEQ ID NO. in Table 1 having all of the corresponding optional promoter fragments identified in Table 3 deleted therefrom. 
     
     
         5 . The isolated nucleic acid molecule of  claim 1 , wherein said nucleic acid molecule is capable of modulating transcription during the developmental times, or in response to a stimulus, or in a cell, tissue, or organ as set forth in Table 2 in the sections “Observed expression pattern” and “Expected expression pattern.” 
     
     
         6 . A vector construct comprising:
 a) a first nucleic acid capable of modulating transcription wherein
 the nucleic acid molecule shows at least 80% sequence identity to a sequence set forth in Table 1; and 
   b) a second nucleic acid having to be transcribed,
 wherein said first and second nucleic acid molecules are heterologous to each other and are operably linked together. 
   
     
     
         7 . The vector construct according to  claim 6 , wherein said nucleic acid comprises a reduced promoter nucleotide sequence having a sequence consisting of a SEQ ID NO. in Table 1 having at least one of the corresponding optional promoter fragments identified in Table 3 deleted therefrom. 
     
     
         8 . The vector construct according to  claim 6 , wherein said nucleic acid comprises a reduced promoter nucleotide sequence having a sequence consisting of a SEQ ID NO. in Table 1 having all of the corresponding optional promoter fragments identified in Table 3 deleted therefrom. 
     
     
         9 . A host cell comprising an isolated nucleic acid molecule according to  claim 1 , wherein said nucleic acid molecule is flanked by exogenous sequence. 
     
     
         10 . The host cell according to  claim 9 , wherein said nucleic acid comprises a reduced promoter nucleotide sequence having a sequence consisting of a SEQ ID NO. in Table 1 having at least one of the corresponding optional promoter fragments identified in Table 3 deleted therefrom. 
     
     
         11 . The host cell according to  claim 9 , wherein said nucleic acid comprises a reduced promoter nucleotide sequence having a sequence consisting of a SEQ ID NO. in Table 1 having all of the corresponding optional promoter fragments identified in Table 3 deleted therefrom. 
     
     
         12 . A host cell comprising a vector construct of  claim 6 . 
     
     
         13 . A method of modulating transcription by combining, in an environment suitable for transcription:
 a) a first nucleic acid molecule capable of modulating transcription
 wherein the nucleic acid molecule shows at least 80% sequence identity to a sequence set forth in Table 1; and 
   b) a second molecule to be transcribed;
 wherein the first and second nucleic acid molecules are heterologous to each other and operably linked together. 
   
     
     
         14 . The method of  claim 13 , wherein said nucleic acid comprises a reduced promoter nucleotide sequence having a sequence consisting of a SEQ ID NO. in Table 1 having at least one of the corresponding optional promoter fragments identified in Table 3 deleted therefrom. 
     
     
         15 . The method of  claim 13 , wherein said nucleic acid comprises a reduced promoter nucleotide sequence having a sequence consisting of a SEQ ID NO. in Table 1 having all of the corresponding optional promoter fragments identified in Table 3 deleted therefrom. 
     
     
         16 . The method according to any one of  claims 13 - 15 , wherein said first nucleic acid molecule is capable of modulating transcription during the developmental times, or in response to a stimuli, or in a cell tissue, or organ as set forth in Table 2 wherein said first nucleic acid molecule is inserted into a plant cell and said plant cell is regenerated into a plant. 
     
     
         17 . A plant comprising a vector construct according to  claim 6 . 
     
     
         18 . A regulatory polynucleotide molecule isolated or identified from  Arabidopsis thaliana , or a complement thereof, or a fragment thereof, or a cis element thereof, wherein said polynucleotide molecule functions to regulate the activity of the S-adenosylmethionine synthetase (SAMS3) gene. 
     
     
         19 . The regulatory polynucleotide molecule of  claim 18  which has the nucleotide sequence of SEQ ID NO: 52. 
     
     
         20 . The regulatory polynucleotide molecule of  claim 18  comprising a nucleic acid sequence that hybridizes under stringent conditions with SEQ ID NO: 52, or any complement thereof, or any fragment thereof, or any cis element thereof. 
     
     
         21 . The regulatory polynucleotide molecule of  claim 18 , or any complement thereof, or any fragment thereof, or any cis element thereof, comprising a nucleic acid sequence wherein the nucleic acid sequence exhibits an 80% or greater identity to SEQ ID NO: 52. 
     
     
         22 . The regulatory polynucleotide molecule of  claim 18 , or any complement thereof, any fragment thereof, or any cis element thereof comprising a nucleic acid sequence wherein the nucleic acid sequence exhibits a 90% or greater identity to SEQ ID NO: 52. 
     
     
         23 . The regulatory polynucleotide molecule of  claim 18 , wherein said regulatory polynucleotide molecule is a promoter. 
     
     
         24 . The promoter of  claim 23 , further described as the polynucleotide molecule of SEQ ID NO: 52. 
     
     
         25 . The regulatory polynucleotide molecule of  claim 18 , wherein said regulatory polynucleotide molecule comprises a leader. 
     
     
         26 . The regulatory polynucleotide molecule of  claim 18 , wherein said regulatory polynucleotide molecule comprises an intron. 
     
     
         27 . A chimeric molecule comprising the regulatory polynucleotide molecule of  claim 18 . 
     
     
         28 . A polynucleotide construct comprising the regulatory polynucleotide molecule of  claim 18 , wherein said regulatory polynucleotide molecule is operably linked to a transcribable polynucleotide molecule. 
     
     
         29 . The polynucleotide construct of  claim 28 , wherein the regulatory polynucleotide molecule comprises the nucleic acid sequence of SEQ ID NO: 52. 
     
     
         30 . The polynucleotide construct of  claim 28 , wherein said regulatory polynucleotide molecule comprises a polynucleotide sequence which exhibits a substantial percent sequence identity of greater than about 80% identity with the nucleic acid sequence of SEQ ID NO: 52. 
     
     
         31 . The polynucleotide construct of  claim 28 , wherein said transcribable polynucleotide molecule is a gene of agronomic interest. 
     
     
         32 . The polynucleotide construct of  claim 28 , wherein said transcribable polynucleotide molecule is a gene controlling the phenotype of a trait selected from the group consisting of: herbicide tolerance, insect control, modified yield, fungal disease resistance, virus resistance, nematode resistance, bacterial disease resistance, plant growth and development, starch production, modified oils production, high oil production, modified fatty acid content, high protein production, fruit ripening, enhanced animal and human nutrition, biopolymers, environmental stress resistance, pharmaceutical peptides and secretable peptides, improved processing traits, improved digestibility, enzyme production, flavor, nitrogen fixation, hybrid seed production, fiber production, and biofuel production. 
     
     
         33 . The polynucleotide construct of  claim 32 , wherein said herbicide tolerance gene is selected from the group consisting of genes that encode for: phosphinothricin acetyltransferase, glyphosate resistant EPSPS, hydroxyphenyl pyruvate dehydrogenase, dalapon dehalogenase, bromoxynil resistant nitrilase, anthranilate synthase, glyphosate oxidoreductase and glyphosate-N-acetyl transferase. 
     
     
         34 . A transgenic plant cell stably transformed with the polynucleotide construct of  claim 28 . 
     
     
         35 . A transgenic plant stably transformed with the polynucleotide construct of  claim 28 . 
     
     
         36 . A seed of said transgenic plant of  claim 25 . 
     
     
         37 . A progeny of the plant of  claim 36 . 
     
     
         38 . The transgenic plant cell of  claim 34 , wherein said plant cell is from a monocotyledonous plant selected from the group consisting of wheat, maize, rye, rice, corn, oat, bailey, turfgrass, sorghum, millet and sugarcane. 
     
     
         39 . The transgenic plant of  claim 35 , wherein said plant is a monocotyledonous plant selected from the group consisting of wheat, maize, rye, rice, corn, oat, barley, turfgrass, sorghum, millet and sugarcane. 
     
     
         40 . The seed of the transgenic plant of  claim 39 . 
     
     
         41 . The transgenic plant cell of  claim 34 , wherein said plant cell is from a dicotyledonous plant selected from the group consisting of tobacco, tomato, potato, soybean, cotton, canola, sunflower and alfalfa. 
     
     
         42 . The transgenic plant of  claim 35 , wherein said plant is a dicotyledonous plant selected from the group consisting of tobacco, tomato, potato, soybean, cotton, canola, sunflower and alfalfa. 
     
     
         43 . The seed of the transgenic plant of  claim 42 . 
     
     
         44 . A method of inhibiting weed growth in a field of transgenic glyphosate-tolerant crop plants comprising planting the transgenic plants transformed with an expression cassette comprising a) a regulatory element polynucleotide molecule isolated or identified from rice, active in a plant cell and operably linked to a polynucleotide molecule encoding a glyphosate tolerance gene; and b) applying glyphosate to the field at an application rate that inhibits the growth of weeds, wherein the growth and yield of the transgenic crop plant is not substantially affected by the glyphosate application. 
     
     
         45 . A regulatory polynucleotide molecule isolated or identified from  Arabidopsis thaliana , or a fragment thereof, wherein said polynucleotide molecule functions to regulate the activity of the S-adenosylmethionine synthetase (SAMS3) gene. 
     
     
         46 . The regulatory polynucleotide molecule of  claim 45  which has the nucleotide sequence of SEQ ID NO: 52. 
     
     
         47 . The regulatory polynucleotide molecule of  claim 45  comprising a nucleic acid sequence that hybridizes under stringent conditions with SEQ ID NO: 52, or any complement thereof, or any fragment thereof. 
     
     
         48 . The regulatory polynucleotide molecule of  claim 45 , comprising a nucleic acid sequence wherein the nucleic acid sequence exhibits an 80% or greater identity to SEQ ID NO: 52, or a fragment thereof. 
     
     
         49 . The regulatory polynucleotide molecule of  claim 45 , comprising a nucleic acid sequence wherein the nucleic acid sequence exhibits a 90% or greater identity to SEQ ID NO: 52, or a fragment thereof. 
     
     
         50 . The regulatory polynucleotide molecule of  claim 45 , wherein said regulatory polynucleotide molecule is a promoter. 
     
     
         51 . The promoter of  claim 50 , further described as the polynucleotide molecule of SEQ ID NO: 52. 
     
     
         52 . The regulatory polynucleotide molecule of  claim 45 , wherein said regulatory polynucleotide molecule is an intron. 
     
     
         53 . A chimeric molecule comprising the regulatory polynucleotide molecule of  claim 45 . 
     
     
         54 . A polynucleotide construct comprising the regulatory polynucleotide molecule of  claim 45 , wherein said regulatory polynucleotide molecule is operably linked to a transcribable polynucleotide molecule. 
     
     
         55 . The polynucleotide construct of  claim 54 , wherein the regulatory polynucleotide molecule comprises the nucleic acid sequence of SEQ ID NO: 52. 
     
     
         56 . The polynucleotide construct of  claim 54 , wherein said regulatory polynucleotide molecule comprises a polynucleotide sequence which exhibits at least 80% sequence identity with SEQ ID NO: 52. 
     
     
         57 . The polynucleotide construct of  claim 54 , wherein said transcribable polynucleotide molecule is a gene of agricultural interest. 
     
     
         58 . The polynucleotide construct of  claim 54 , wherein said transcribable polynucleotide molecule is a gene controlling the phenotype of a trait selected from the group consisting of: herbicide tolerance, insect control, modified yield, fungal disease resistance, virus resistance, nematode resistance, plant growth and development, starch production, modified oils production, high oil production, fruit ripening, environmental stress resistance, and nitrogen fixation. 
     
     
         59 . The polynucleotide construct of  claim 58 , wherein said herbicide tolerance gene is selected from the group consisting of genes that encode for genes that are resistant to phosphinothricin, glyphosate or bromoxynil. 
     
     
         60 . A transgenic plant cell stably transformed with the polynucleotide construct of  claim 54 . 
     
     
         61 . A transgenic plant stably transformed with the polynucleotide construct of  claim 54 . 
     
     
         62 . A seed of said transgenic plant of  claim 64 . 
     
     
         63 . A progeny of the plant of  claim 62 . 
     
     
         64 . The transgenic plant cell of  claim 60 , wherein said plant cell is a plant selected from the group consisting of wheat and corn. 
     
     
         65 . The transgenic plant of  claim 61 , wherein said plant is a plant selected from the group consisting of wheat and corn. 
     
     
         66 . The seed of the transgenic plant of  claim 65 . 
     
     
         67 . A polynucleotide molecule capable of modulating transcription which has the nucleotide sequence of SEQ ID NO: 52, or a fragment thereof. 
     
     
         68 . The polynucleotide molecule of  claim 67  which has the nucleotide sequence of SEQ ID NO: 52. 
     
     
         69 . The polynucleotide molecule of  claim 67  comprising a nucleic acid sequence that hybridizes tinder stringent conditions with SEQ ID NO: 52. 
     
     
         70 . The polynucleotide molecule of  claim 67 , comprising a nucleic acid sequence wherein the nucleic acid sequence exhibits at least 80% sequence identity to SEQ ID NO: 52, or a fragment thereof. 
     
     
         71 . The polynucleotide molecule of  claim 67 , comprising a nucleic acid sequence wherein the nucleic acid sequence exhibits at least 90% sequence identity to SEQ ID NO: 52, or any fragment thereof. 
     
     
         72 . The polynucleotide molecule of  claim 67 , wherein said polynucleotide molecule is a promoter. 
     
     
         73 . The promoter of  claim 72 , further described as the polynucleotide molecule of SEQ ID NO: 52. 
     
     
         74 . A chimeric molecule comprising the polynucleotide molecule of  claim 67 . 
     
     
         75 . A polynucleotide construct comprising a first polynucleotide molecule of  claim 67 , operably linked to a transcribable polynucleotide molecule. 
     
     
         76 . The polynucleotide construct of  claim 75 , wherein the polynucleotide molecule comprises the nucleic acid sequence of SEQ ID NO: 52. 
     
     
         77 . The polynucleotide construct of  claim 75 , wherein said first polynucleotide molecule comprises a polynucleotide sequence which exhibits at least 80% sequence identity with the nucleic acid sequence of SEQ ID NO: 52. 
     
     
         78 . The polynucleotide construct of  claim 75 , wherein said transcribable polynucleotide molecule is a gene of agricultural interest. 
     
     
         79 . The polynucleotide construct of  claim 75 , wherein said transcribable polynucleotide molecule is a gene controlling the phenotype of a trait selected from the group consisting of: herbicide tolerance, insect control, modified yield, fungal disease resistance, virus resistance, nematode resistance, plant growth and development, starch production, modified oils production, high oil production, fruit ripening, and nitrogen fixation. 
     
     
         80 . The polynucleotide construct of  claim 79 , wherein said herbicide tolerance gene is selected from the group consisting of genes that encode for genes that confer resistance to phosphinothricin, glyphosate or bromoxynil. 
     
     
         81 . A transgenic plant cell stably transformed with the polynucleotide construct of  claim 75 . 
     
     
         82 . A transgenic plant stably transformed with the polynucleotide construct of  claim 75 . 
     
     
         83 . A seed of said transgenic plant of  claim 82 . 
     
     
         84 . A progeny of the plant of  claim 82 . 
     
     
         85 . The transgenic plant cell of  claim 81 , wherein said plant cell is a cell selected from the group consisting of wheat and corn. 
     
     
         86 . The transgenic plant of  claim 82 , wherein said plant is a plant selected from the group consisting of wheat and corn. 
     
     
         87 . The seed of the transgenic plant of  claim 86 . 
     
     
         88 . A transgenic plant cell stably transformed with the polynucleotide construct of  claim 76 . 
     
     
         89 . A transgenic plant stably transformed with polynucleotide construct of  claim 76 . 
     
     
         90 . The seed of the transgenic plant of  claim 89 . 
     
     
         91 . A progeny of the plant of  claim 89 . 
     
     
         92 . The transgenic plant cell of  claim 88 , wherein said plant cell is a cell selected from the group consisting of wheat and corn. 
     
     
         93 . The transgenic plant of  claim 89 , wherein said plant is a plant selected from the group consisting of wheat and corn. 
     
     
         94 . The seed of the transgenic plant of  claim 93 .