Chimeric promoters and methods of use

Abstract

Compositions and methods comprising promoters from the 4-hydroxyphenylpyruvate dioxygenase (HPPD) gene and active variants and fragments thereof, as well as chimeric promoters employing regulatory regions of the HPPD promoters are provided. Further provided are expression cassettes and plants comprising the various promoters disclosed herein operably linked to a polynucleotide of interest. Methods employing the various promoters described herein to modulate the expression of polynucleotides of interest are further provided.

1 . A chimeric promoter construct comprising
 a first polynucleotide comprising a regulatory region of a 4-hydroxyphenylpyruvate dioxygenase (HPPD) promoter operably linked to a second polynucleotide comprising a heterologous core promoter functional in a plant,   wherein said regulatory region of the HPPD promoter comprises   a) a polynucleotide having at least 90% sequence identity to any one of SEQ ID NO: 2, 3, 4, 11, or 20; or   b) a polynucleotide having at least 90% sequence identity to any one of SEQ ID NO: 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, 18, or 19;   wherein said core promoter modulates the regulatory activity of said regulatory region of the HPPD promoter when compared to the regulatory activity of said regulatory region of the HPPD promoter alone;   wherein said chimeric promoter has transcriptional regulatory activity in a plant.   
     
     
         2 . (canceled) 
     
     
         3 . The chimeric promoter construct of  claim 1 , wherein said transcriptional regulatory activity of said regulatory region of the HPPD promoter in the absence of said core promoter comprises less than 10% of the transcriptional regulatory activity of the HPPD promoter set forth in SEQ ID NO: 1. 
     
     
         4 . The chimeric promoter construct of  claim 1 , wherein said transcriptional regulatory activity of said regulatory region of the HPPD promoter in the absence of said core promoter comprises at least 10% of the regulatory activity of the HPPD promoter as set forth in SEQ ID NO: 1. 
     
     
         5 . The chimeric promoter construct of  claim 1 , wherein said regulatory region of the HPPD promoter comprises a deletion selected from the group consisting of:
 (a) a deletion of a TATA motif; or   (b) a deletion of at least one of the TATA1, TATA2, TATA3, TATA4 or TATA5 motifs.   
     
     
         6 . (canceled) 
     
     
         7 . The chimeric promoter construct of  claim 1 , wherein said regulatory region of the HPPD promoter comprises at least one or more alterations in at least one of the TATA1, TATA2, TATA3, TATA4 or TATA5 elements. 
     
     
         8 - 12 . (canceled) 
     
     
         13 . The chimeric promoter construct of  claim 1 , wherein said core promoter comprises
 a) the polynucleotide set forth in SEQ ID NO:71;   b) a polynucleotide having at least 90% sequence identity to SEQ ID NO:71, where said polynucleotide continues to have core promoter activity;   c) a polynucleotide comprising a fragment comprising at least 30 consecutive nucleotides of SEQ ID NO: 71;   d) the polynucleotide set forth in SEQ ID NO: 21; or   e) the polynucleotide set forth in SEQ ID NO: 83.   
     
     
         14 . The chimeric promoter construct of  claim 13 , wherein said core promoter further comprises
 a) a second polynucleotide as set forth in SEQ ID NO:72;   b) a second polynucleotide having at least 90% sequence identity to SEQ ID NO:72, where said second polynucleotide modulates the activity of the core promoter; or   c) a second polynucleotide comprising a fragment comprising at least 20 consecutive nucleotides of SEQ ID NO: 72.   
     
     
         15 . The chimeric promoter construct of  claim 14 , wherein said core promoter further comprises
 a) the polynucleotide set forth in SEQ ID NO:73;   b) a polynucleotide having at least 90% sequence identity to SEQ ID NO:73, where said polynucleotide continues to have core promoter activity;   c) a polynucleotide comprising a fragment comprising at least 30 consecutive nucleotides of SEQ ID NO: 73; or   d) the polynucleotide set forth in SEQ ID NO: 22.   
     
     
         16 . The chimeric promoter construct of  claim 1 , wherein the chimeric promoter comprises
 a) the sequence set forth in SEQ ID NO: 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 74, 75, 76, 77, or 78;   b) a sequence having at least 85% sequence identity to the sequence set 15 forth in SEQ ID NO: 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 74, 75, 76, 77, or 78;   c) a polynucleotide comprising a fragment comprising at least 300 consecutive nucleotides of SEQ ID NO: 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 74, 75, 76, 77, or 78; or   d) a polynucleotide comprising a fragment comprising at least 300 consecutive nucleotides of a sequence having at least 85% sequence identity to the sequence set forth in SEQ ID NO: 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 74, 75, 76, 77, or 78.   
     
     
         17 . (canceled) 
     
     
         18 . (canceled) 
     
     
         19 . (canceled) 
     
     
         20 . (canceled) 
     
     
         21 . A plant having stably incorporated into its genome at least one expression cassette comprising a promoter operably linked to a polynucleotide of interest, wherein said promoter comprises the chimeric promoter construct of  claim 1 . 
     
     
         22 . The plant of  claim 21 , wherein said plant is a dicot. 
     
     
         23 . (canceled) 
     
     
         24 . The plant of  claim 22 , wherein said dicot is soybean,  Brassica , sunflower, cotton, or alfalfa. 
     
     
         25 . The plant of  claim 21 , wherein said plant is a monocot. 
     
     
         26 . The plant of  claim 25 , wherein said monocot is maize, wheat, rice, barley, sorghum, or rye. 
     
     
         27 . A method of regulating the expression of a polynucleotide of interest, said method comprising stably incorporating in the genome of a plant or plant cell the polynucleotide sequence of interest operably linked to a promoter wherein said promoter comprises the chimeric polynucleotide of  claim 1 . 
     
     
         28 . The method of  claim 27 , wherein said plant is a dicot. 
     
     
         29 . (canceled) 
     
     
         30 . The method of  claim 28 , wherein said dicot is soybean,  Brassica , sunflower, cotton, or alfalfa. 
     
     
         31 . The method of  claim 27 , wherein said plant is a monocot. 
     
     
         32 . The method of  claim 31 , wherein said monocot is maize, wheat, rice, barley, sorghum, or rye. 
     
     
         33 . A polynucleotide comprising a promoter operably linked to a heterologous polynucleotide of interest, wherein the promoter is capable of regulating transcription of the heterologous polynucleotide of interest, wherein the promoter comprises:
 (a)   a polynucleotide comprising a nucleotide sequence having at least 85% sequence identity to SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 15 17, 18, 19, 20, 74,   (b) a polynucleotide comprising a nucleotide sequence having at least 85% sequence identity to a fragment comprising at least 300 consecutive nucleotides of SEQ ID NO: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 74, 75, or 76.   
     
     
         34 . (canceled) 
     
     
         35 . (canceled) 
     
     
         36 . (canceled) 
     
     
         37 . (canceled) 
     
     
         38 . A plant having stably incorporated into its genome at least one expression cassette comprising a polynucleotide of interest operably linked to a promoter, wherein said promoter comprises the polynucleotide of  claim 33 . 
     
     
         39 . The plant of  claim 38 , wherein said plant is a dicot. 
     
     
         40 . (canceled) 
     
     
         41 . The plant of  claim 39 , wherein said dicot is soybean,  Brassica , sunflower, cotton, or alfalfa. 
     
     
         42 . The plant of  claim 38 , wherein said plant is a monocot. 
     
     
         43 . The plant of  claim 42 , wherein said monocot is maize, wheat, rice, barley, sorghum, or rye. 
     
     
         44 . A method of expressing a polynucleotide of interest, said method comprising stably incorporating in the genome of a plant or plant cell the polynucleotide of interest operably linked to a promoter, wherein said promoter comprises the polynucleotide of  claim 33 . 
     
     
         45 . The method of  claim 44 , wherein said plant is a dicot. 
     
     
         46 . (canceled) 
     
     
         47 . The method of  claim 45 , wherein said dicot is soybean,  Brassica , sunflower, cotton, or alfalfa. 
     
     
         48 . The method of  claim 44 , wherein said plant is a monocot. 
     
     
         49 . The method of  claim 48 , wherein said monocot is maize, wheat, rice, barley, sorghum, or rye.