Pyrimidine box gene transcriptions

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Editor-In-Chief: Henry A. Hoff

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This cornfield is in South Africa. Credit: Lotus Head from Johannesburg, Gauteng, South Africa.{{free media}}

"Functional analyses of a number of hydrolase gene promoters, induced by gibberellin (GA) in aleurone cells following germination, have identified a GA-responsive complex as a tripartite element containing a pyrimidine box motif 5′-CCTTTT-3′."[1]

"The pyrimidine box is another promoter element that is observed in cereal GA-responsive promoters examined thus far (Huang et al., 1990). Mutations on the pyrimidine box caused the reduction of the GA induction with a lesser magnitude than those of GARE in the GA-treated aleurone (Gubler and Jacobsen, 1992; Rogers and Rogers, 1992). The pyrimidine box alone could not confer the hormone responsiveness to the minimal promoter of the cauliflower mosaic virus 35S (CaMV35S), suggesting accessory roles of the pyrimidine box on the transcription response to GA (Skriver et al., 1991)."[2]

"[A]leurone proteins that recognized the pyrimidine box sequence [are] from barley (BPBF; Mena et al., 2002) and rice (Oryza sativa; OsDOF3; Washio, 2001)."[2]

"A member of Dof proteins, prolamine box-binding factors PBF that were originally identified to be transcription factors regulating the expression of genes for stored proteins in developing seeds (Vicente-Carbajosa et al., 1997; Mena et al., 1998), BPBF and OsDOF3 are likely to be a pyrimidine box-binding protein in the germinated aleurone."[2]

"OsDOF3, binding the pyrimidine box, affected the DNA binding of GAMYB to GARE".[2]

"Functional promoter analysis using transgenic rice seeds has confirmed that the 5'-regulatory region extending from -232 (nucleotide position relative to the site for transcription initiation) to +31 is sufficient for hormonal regulation by GA (Itoh et al., 1995), along which are found the distal (Pyr-1, -312) and proximal pyrimidine boxes (Pyr-2, -214), GARE (-148), and three potential sites for the Dof binding (D-1, -191; D-2, -109; D-3, -78; [on the diagram in the GA responsive complexes section above]; Huang et al., 1990)."[2]

"The upstream portion from the RAmy1A promoter (-380 to +27) had a stimulatory effect on the GA-induced expression of the reporter gene in transfected aleurone cells."[2]

"The drastic loss of the GA induction associated with a mutation on GARE (M4) further verifies the importance of this motif in the GA-regulated expression of genes. Other mutations of the proximal pyrimidine box (M2) and one site for the Dof binding (M5) also reduced the GA-induced activities to 48% and 54% of the wild-type sequence, respectively, but the effects were not as marked as seen when GARE was mutated."[2]

"Sequence analysis shows that the OsDof3 cDNA encodes a 371-amino acid polypeptide related to the PBF factors of cereal plants. The predicted amino acid sequence of OsDOF3 aligns well with those of maize (Zea mays; Vicente-Carbajosa et al., 1997), wheat (Triticum aestivum), and barley PBF proteins (Mena et al., 1998; [...]). The N-terminal sequence of OsDOF3 contains four Cys residues reminiscent of the Dof zinc finger and shows around 80% sequence identities with PBFs, whereas the C-terminal parts are divergent showing several insertions and deletions."[2]

"Pentanucleotide sequence from the pyrimidine box (CTTTT; Huang et al., 1990) and D-3 (AAAAG) is capable of matching a favored substrate selected by in vitro DNA binding of maize Dof proteins (CTTTT or AAAAG; Yanagisawa and Schmidt, 1999). These results indicate preferential binding of OsDOF3 to two pyrimidine box and D-3 motifs in the RAmy1A promoter context."[2]

Gibberellic acid responsive complexes

"Although this GARC [GA responsive complex] may not always be tripartite, most often it includes three sequence motifs, the TAACAAA box or GA responsive element (GARE), the pyrimidine box CCTTTT, and the TATCCAC box (Skriver et al., 1991;Gubler and Jacobsen, 1992; Rogers et al., 1994)."[1]

"Some other cis-acting elements, such as pyrimidine boxes (GGTTTT) and TAT boxes (TATCCAT), are usually present in the vicinity of the GARE sequence of genes regulated by GA in cereal aleurone cells (Gubler and Jacobsen 1992; Cercos et al. 1999; Tsuji et al. 2006)."[3]

"Given the general observations that a couple of the promoter motifs, GARE and the pyrimidine box, always exist in a close distance in the reported GA-responsive promoters (Huang et al., 1990), the synergistic effect on RAmy1A promoter activation are likely to be mediated through protein-protein interaction."[2]

P-boxes

The "complementary strand of the pyrimidine box element (5′-CTTTT-3′) in GA-induced hydrolase gene promoters was identical to the core sequence (5′-AAAAG-3′) recognized by PBF in prolamin gene promoters (P-box: 5′-T/AAAAG-3′; Vicente-Carbajosa et al., 1997; Mena et al., 1998; Yanagisawa and Schmidt, 1999)".[1]

Pyrimidine box samplings

For the Basic programs (starting with SuccessablesPyr.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), including extending the number of nts from 958 to 4445, the programs are, are looking for, and found:

  1. negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesPyr--.bas, looking for CCTTTT, 3, CCTTTT at 2459, CCTTTT at 2927, CCTTTT at 2968,
  2. negative strand, positive direction (from ZNF497 to A1BG) is SuccessablesPyr-+.bas, looking for CCTTTT, 1, CCTTTT at 135,
  3. positive strand, negative direction is SuccessablesPyr+-.bas, looking for CCTTTT, 0,
  4. positive strand, positive direction is SuccessablesPyr++.bas, looking for CCTTTT, 1, CCTTTT at 291,
  5. complement, negative strand, negative direction is SuccessablesPyrc--.bas, looking for GGAAAA, 0,
  6. complement, negative strand, positive direction is SuccessablesPyrc-+.bas, looking for GGAAAA, 1, GGAAAA at 291,
  7. complement, positive strand, negative direction is SuccessablesPyrc+-.bas, looking for GGAAAA, 3, GGAAAA at 2459, GGAAAA at 2927, GGAAAA at 2968,
  8. complement, positive strand, positive direction is SuccessablesPyrc++.bas, looking for GGAAAA, 1, GGAAAA at 135,
  9. inverse complement, negative strand, negative direction is SuccessablesPyrci--.bas, looking for AAAAGG, 0,
  10. inverse complement, negative strand, positive direction is SuccessablesPyrci-+.bas, looking for AAAAGG, 0,
  11. inverse complement, positive strand, negative direction is SuccessablesPyrci+-.bas, looking for AAAAGG, 4, AAAAGG at 105, AAAAGG at 1107, AAAAGG at 3345, AAAAGG at 3441,
  12. inverse complement, positive strand, positive direction is SuccessablesPyrci++.bas, looking for AAAAGG, 0,
  13. inverse, negative strand, negative direction, is SuccessablesPyri--.bas, looking for TTTTCC, 4, TTTTCC at 105, TTTTCC at 1107, TTTTCC at 3345, TTTTCC at 3441,
  14. inverse, negative strand, positive direction, is SuccessablesPyri-+.bas, looking for 3'-TTTTCC-5', 0,
  15. inverse, positive strand, negative direction, is SuccessablesPyri+-.bas, looking for 3'-TTTTCC-5', 0,
  16. inverse, positive strand, positive direction, is SuccessablesPyri++.bas, looking for 3'-TTTTCC-5', 0.

Pyr (4560-2846) UTRs

  1. Negative strand, negative direction: CCTTTT at 2968, CCTTTT at 2927.
  2. Positive strand, negative direction: AAAAGG at 3441, AAAAGG at 3345.

Pyr negative direction (2596-1) distal promoters

  1. Negative strand, negative direction: CCTTTT at 2459.
  2. Positive strand, negative direction: AAAAGG at 1107, AAAAGG at 105.

Pyr positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: CCTTTT at 135.
  2. Positive strand, positive direction: CCTTTT at 291.

Pyr random dataset samplings

  1. Pyrr0: 2, CCTTTT at 1275, CCTTTT at 221.
  2. Pyrr1: 4, CCTTTT at 3646, CCTTTT at 2407, CCTTTT at 1273, CCTTTT at 654.
  3. Pyrr2: 3, CCTTTT at 3664, CCTTTT at 3219, CCTTTT at 858.
  4. Pyrr3: 2, CCTTTT at 4187, CCTTTT at 1704.
  5. Pyrr4: 5, CCTTTT at 2203, CCTTTT at 2013, CCTTTT at 1732, CCTTTT at 1404, CCTTTT at 594.
  6. Pyrr5: 3, CCTTTT at 4531, CCTTTT at 2355, CCTTTT at 1793.
  7. Pyrr6: 4, CCTTTT at 4226, CCTTTT at 3672, CCTTTT at 3289, CCTTTT at 3282.
  8. Pyrr7: 3, CCTTTT at 3580, CCTTTT at 3174, CCTTTT at 1990.
  9. Pyrr8: 5, CCTTTT at 3414, CCTTTT at 3060, CCTTTT at 3011, CCTTTT at 2253, CCTTTT at 1862.
  10. Pyrr9: 3, CCTTTT at 1908, CCTTTT at 1030, CCTTTT at 134.
  11. Pyrr0ci: 1, AAAAGG at 3659.
  12. Pyrr1ci: 2, AAAAGG at 4013, AAAAGG at 3177.
  13. Pyrr2ci: 4, AAAAGG at 1440, AAAAGG at 474, AAAAGG at 252, AAAAGG at 110.
  14. Pyrr3ci: 3, AAAAGG at 3596, AAAAGG at 2600, AAAAGG at 2276.
  15. Pyrr4ci: 0.
  16. Pyrr5ci: 2, AAAAGG at 637, AAAAGG at 227.
  17. Pyrr6ci: 2, AAAAGG at 4454, AAAAGG at 972.
  18. Pyrr7ci: 3, AAAAGG at 4549, AAAAGG at 1933, AAAAGG at 1277.
  19. Pyrr8ci: 2, AAAAGG at 2390, AAAAGG at 504.
  20. Pyrr9ci: 2, AAAAGG at 1410, AAAAGG at 588.

Pyrr arbitrary (evens) (4560-2846) UTRs

  1. Pyrr2: CCTTTT at 3664, CCTTTT at 3219.
  2. Pyrr6: CCTTTT at 4226, CCTTTT at 3672, CCTTTT at 3289, CCTTTT at 3282.
  3. Pyrr8: CCTTTT at 3414, CCTTTT at 3060, CCTTTT at 3011.
  4. Pyrr0ci: AAAAGG at 3659.
  5. Pyrr6ci: AAAAGG at 4454, AAAAGG at 972.

Pyrr alternate (odds) (4560-2846) UTRs

  1. Pyrr1: CCTTTT at 3646.
  2. Pyrr3: CCTTTT at 4187.
  3. Pyrr5: CCTTTT at 4531.
  4. Pyrr7: CCTTTT at 3580, CCTTTT at 3174.
  5. Pyrr1ci: AAAAGG at 4013, AAAAGG at 3177.
  6. Pyrr3ci: AAAAGG at 3596.
  7. Pyrr7ci: AAAAGG at 4549.

Pyrr alternate negative direction (odds) (2811-2596) proximal promoters

  1. Pyrr3ci: AAAAGG at 2600.

PYRr arbitrary positive direction (odds) (4265-4050) proximal promoters

  1. Pyrr3: CCTTTT at 4187.

Pyrr alternate positive direction (evens) (4265-4050) proximal promoters

  1. Pyrr6: CCTTTT at 4226.

Pyrr arbitrary negative direction (evens) (2596-1) distal promoters

  1. Pyrr0: CCTTTT at 1275, CCTTTT at 221.
  2. Pyrr2: CCTTTT at 858.
  3. Pyrr4: CCTTTT at 2203, CCTTTT at 2013, CCTTTT at 1732, CCTTTT at 1404, CCTTTT at 594.
  4. Pyrr8: CCTTTT at 2253, CCTTTT at 1862.
  5. Pyrr2ci: AAAAGG at 1440, AAAAGG at 474, AAAAGG at 252, AAAAGG at 110.
  6. Pyrr6ci: AAAAGG at 972.
  7. Pyrr8ci: AAAAGG at 2390, AAAAGG at 504.

Pyrr alternate negative direction (odds) (2596-1) distal promoters

  1. Pyrr1: CCTTTT at 2407, CCTTTT at 1273, CCTTTT at 654.
  2. Pyrr3: CCTTTT at 1704.
  3. Pyrr5: CCTTTT at 2355, CCTTTT at 1793.
  4. Pyrr7: CCTTTT at 1990.
  5. Pyrr9: CCTTTT at 1908, CCTTTT at 1030, CCTTTT at 134.
  6. Pyrr3ci: AAAAGG at 2276.
  7. Pyrr5ci: AAAAGG at 637, AAAAGG at 227.
  8. Pyrr7ci: AAAAGG at 1933, AAAAGG at 1277.
  9. Pyrr9ci: AAAAGG at 1410, AAAAGG at 588.

Pyrr arbitrary positive direction (odds) (4050-1) distal promoters

  1. Pyrr1: CCTTTT at 3646, CCTTTT at 2407, CCTTTT at 1273, CCTTTT at 654.
  2. Pyrr3: CCTTTT at 1704.
  3. Pyrr5: CCTTTT at 2355, CCTTTT at 1793.
  4. Pyrr7: CCTTTT at 3580, CCTTTT at 3174, CCTTTT at 1990.
  5. Pyrr9: CCTTTT at 1908, CCTTTT at 1030, CCTTTT at 134.
  6. Pyrr1ci: AAAAGG at 4013, AAAAGG at 3177.
  7. Pyrr3ci: AAAAGG at 3596, AAAAGG at 2600, AAAAGG at 2276.
  8. Pyrr5ci: AAAAGG at 637, AAAAGG at 227.
  9. Pyrr7ci: AAAAGG at 1933, AAAAGG at 1277.
  10. Pyrr9ci: AAAAGG at 1410, AAAAGG at 588.

Pyrr alternate positive direction (evens) (4050-1) distal promoters

  1. Pyrr0: CCTTTT at 1275, CCTTTT at 221.
  2. Pyrr2: CCTTTT at 3664, CCTTTT at 3219, CCTTTT at 858.
  3. Pyrr4: CCTTTT at 2203, CCTTTT at 2013, CCTTTT at 1732, CCTTTT at 1404, CCTTTT at 594.
  4. Pyrr6: CCTTTT at 3672, CCTTTT at 3289, CCTTTT at 3282.
  5. Pyrr8: CCTTTT at 3414, CCTTTT at 3060, CCTTTT at 3011, CCTTTT at 2253, CCTTTT at 1862.
  6. Pyrr0ci: AAAAGG at 3659.
  7. Pyrr2ci: AAAAGG at 1440, AAAAGG at 474, AAAAGG at 252, AAAAGG at 110.
  8. Pyrr6ci: AAAAGG at 972.
  9. Pyrr8ci: AAAAGG at 2390, AAAAGG at 504.

Pyrimidine box analysis and results

Main article: Complex locus A1BG and ZNF497 § Pyrimidine boxes

"Functional analyses of a number of hydrolase gene promoters, induced by gibberellin (GA) in aleurone cells following germination, have identified a GA-responsive complex as a tripartite element containing a pyrimidine box motif 5′-CCTTTT-3′."[1]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 4 2 2 2
Randoms UTR arbitrary negative 12 10 1.2 1.05 ± 0.15
Randoms UTR alternate negative 9 10 0.9 1.05 ± 0.15
Reals Core negative 0 2 0 0
Randoms Core arbitrary negative 0 10 0 0
Randoms Core alternate negative 0 10 0 0
Reals Core positive 0 2 0 0
Randoms Core arbitrary positive 0 10 0 0
Randoms Core alternate positive 0 10 0 0
Reals Proximal negative 0 2 0 0
Randoms Proximal arbitrary negative 0 10 0 0.05
Randoms Proximal alternate negative 1 10 0.1 0.05
Reals Proximal positive 0 2 0 0
Randoms Proximal arbitrary positive 1 10 0.1 0.1
Randoms Proximal alternate positive 1 10 0.1 0.1
Reals Distal negative 3 2 1.5 1.5
Randoms Distal arbitrary negative 17 10 1.7 1.7
Randoms Distal alternate negative 17 10 1.7 1.7
Reals Distal positive 2 2 1 1
Randoms Distal arbitrary positive 24 10 2.4 2.5
Randoms Distal alternate positive 26 10 2.6 2.5

Comparison:

The occurrences of real Pyr UTRs are greater than the randoms, while the distals are less than the randoms. This suggests that the real Pyrs are likely active or activable.

Acknowledgements

The content on this page was first contributed by: Henry A. Hoff.

Initial content for this page in some instances came from Wikiversity.

See also

References

  1. ↑ 1.0 1.1 1.2 1.3 Montaña Mena, Francisco Javier Cejudo, Ines Isabel-Lamoneda and Pilar Carbonero (1 September 2002). "A Role for the DOF Transcription Factor BPBF in the Regulation of Gibberellin-Responsive Genes in Barley Aleurone". Plant Physiology. 130 (1): 111–9. doi:10.1104/pp.005561. Retrieved 2017-02-19.
  2. ↑ 2.0 2.1 2.2 2.3 2.4 2.5 2.6 2.7 2.8 2.9 Kenji Washio (October 2003). "Functional Dissections between GAMYB and Dof Transcription Factors Suggest a Role for Protein-Protein Associations in the Gibberellin-Mediated Expression of the RAmy1A Gene in the Rice Aleurone" (PDF). Plant Physiology. 133 (2): 850–63. doi:10.1104/pp.103.027334. Retrieved 10 October 2018.
  3. ↑ Liu-Min Fan, Xiaoyan Feng, Yu Wang and Xing Wang Deng (2007). "Gibberellin Signal Transduction in Rice". Journal of Integrative Plant Biology. 49 (6): 731−741. doi:10.1111/j.1744-7909.2007.00511.x. Retrieved 16 October 2018.

External links


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