Prolamin box gene transcriptions

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Editor-In-Chief: Henry A. Hoff

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A field of maize (corn) is shown. Credit: Löwe 48.{{free media}}

"The BPBF [barley prolamin-box (P-box) binding factor] expressed in bacteria as a GST-fusion binds a P-box 5′-TGTAAAG-3′ containing oligonucleotide derived from the promoter region of anHor2gene."[1]

"The primary structure of hordein [barley prolamins] polypeptides is closely related to that of prolamins from other grass species from the Pooideae subfamily, such as wheat and rye (Shewry & Tatham 1990;Shewry et al. 1995)."[1]

Consensus sequences

"The close evolutionary relationship is also manifested by the conservation of a putative regulatory element in their gene promoters, the endosperm box (Forde et al. 1985;Kreis et al. 1985). This conserved region consists of two motifs, a 7 bp element (5′TGTAAAG3′) termed the Prolamin Box (P-box) or endosperm motif (EM) followed at a distance of up to 8 nucleotides by the GCN4-like motif (GLM) which has the 5′(G/A)TGA(G/C)TCA(T/C)3′ consensus sequence (reviewed by Müller et al. 1995)."[1]

"The main cis-element present in their promoters is an endosperm-specific box [19,20], which consists of two motifs: a GLM (GCN4-like motif) (5′ G(A)TGA(G) GTCAT 3′) that shares homology with yeast GCN4 [21], and a 7 bp P-box (Prolamin box) (5′TGTAAAG3′) [22–24]."[2]

Prolamin box sampling

For the Basic programs (starting with SuccessablesProl.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 (+), the programs are, are looking for, and found:

  1. negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesProl--.bas, looking for TG(A/T)AAAG, 1, TGTAAAG-5 at 2884,
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesProl-+.bas, looking for TG(A/T)AAAG, 1, TGAAAAG at 3928,
  3. positive strand in the negative direction is SuccessablesProl+-.bas, looking for TG(A/T)AAAG, 1, TGAAAAG at 1627,
  4. positive strand in the positive direction is SuccessablesProl++.bas, looking for TG(A/T)AAAG, 1, TGAAAAG at 2275, and complement.
  5. complement, negative strand, negative direction is SuccessablesProlc--.bas, looking for AC(A/T)TTTC, 1, ACTTTTC at 1627,
  6. complement, negative strand, positive direction is SuccessablesProlc-+.bas, looking for AC(A/T)TTTC, ACTTTC at 3928,
  7. complement, positive strand, negative direction is SuccessablesProlc+-.bas, looking for AC(A/T)TTTC, 1, ACATTTC at 2884,
  8. complement, positive strand, positive direction is SuccessablesProlc++.bas, looking for AC(A/T)TTTC, 1, ACTTTTC at 3928,
  9. inverse complement, negative strand, negative direction is SuccessablesProlci--.bas, looking for CTTT(A/T)CA, 0,
  10. inverse complement, negative strand, positive direction is SuccessablesProlci-+.bas, looking for CTTT(A/T)CA, 0,
  11. inverse complement, positive strand, negative direction is SuccessablesProlci+-.bas, looking for CTTT(A/T)CA, 0,
  12. inverse complement, positive strand, positive direction is SuccessablesProlci++.bas, looking for CTTT(A/T)CA, 0,
  13. inverse, negative strand, negative direction, is SuccessablesProli--.bas, looking for GAAA(A/T)GT, 0,
  14. inverse, negative strand, positive direction, is SuccessablesProli-+.bas, looking for GAAA(A/T)GT, 0,
  15. inverse, positive strand, negative direction, is SuccessablesProli+-.bas, looking for GAAA(A/T)GT, 0,
  16. inverse, positive strand, positive direction, is SuccessablesProli++.bas, looking for GAAA(A/T)GT, 0.

Prol (4560-2846) UTRs

  1. Negative strand, negative direction: TGTAAAG at 2884.

Prol positive direction (4445-4265) core promoters

  1. Negative strand, positive direction: TGAAAAG at 3928.

Prol negative direction (2596-1) distal promoters

  1. Positive strand, negative direction: TGAAAAG at 1627.

Prol positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: TGAAAAG at 3928.
  2. Positive strand, positive direction: TGAAAAG at 2275.

Prolamin box random dataset samplings

  1. Prolr0: 0.
  2. Prolr1: 0.
  3. Prolr2: 1, TGAAAAG at 1439.
  4. Prolr3: 2, TGTAAAG at 3061, TGAAAAG at 2275.
  5. Prolr4: 0.
  6. Prolr5: 0.
  7. Prolr6: 1, TGTAAAG at 2630.
  8. Prolr7: 0.
  9. Prolr8: 2, TGAAAAG at 891, TGAAAAG at 503.
  10. Prolr9: 0.
  11. Prolr0ci: 0.
  12. Prolr1ci: 1, CTTTACA at 526.
  13. Prolr2ci: 1, CTTTACA at 1186.
  14. Prolr3ci: 2, CTTTACA at 3641, CTTTACA at 319.
  15. Prolr4ci: 1, CTTTTCA at 474.
  16. Prolr5ci: 1, CTTTTCA at 1267.
  17. Prolr6ci: 0.
  18. Prolr7ci: 0.
  19. Prolr8ci: 0.
  20. Prolr9ci: 1, CTTTTCA at 2695.

Prolr alternate (odds) (4560-2846) UTRs

  1. Prolr3: TGTAAAG at 3061.
  2. Prolr3ci: CTTTACA at 3641

Prolr arbitrary negative direction (evens) (2811-2596) proximal promoters

  1. Prolr6: TGTAAAG at 2630.

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

  1. Prolr9ci: CTTTTCA at 2695.

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

  1. Prolr2: TGAAAAG at 1439.
  2. Prolr8: TGAAAAG at 891, TGAAAAG at 503.
  3. Prolr2ci: CTTTACA at 1186.
  4. Prolr4ci: CTTTTCA at 474.

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

  1. Prolr3: TGAAAAG at 2275.
  2. Prolr1ci: CTTTACA at 526.
  3. Prolr3ci: CTTTACA at 319.
  4. Prolr5ci: CTTTTCA at 1267.

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

  1. Prolr3: TGTAAAG at 3061, TGAAAAG at 2275.
  2. Prolr1ci: CTTTACA at 526.
  3. Prolr3ci: CTTTACA at 3641, CTTTACA at 319.
  4. Prolr5ci: CTTTTCA at 1267.
  5. Prolr9ci: CTTTTCA at 2695.

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

  1. Prolr2: TGAAAAG at 1439.
  2. Prolr6: TGTAAAG at 2630.
  3. Prolr8: TGAAAAG at 891, TGAAAAG at 503.
  4. Prolr2ci: CTTTACA at 1186.
  5. Prolr4ci: CTTTTCA at 474.

Prolamin box analysis and results

Main article: Complex locus A1BG and ZNF497 § Prols

Modified prolamin box

Modified prolamin box: the 7 bp element (TGTAAAG) termed the Prolamin Box (P-box),[1] modified to TG(A/T)AAAG.

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 1 2 0.5 0.5 ± 0.5 (--1,+-0)
Randoms UTR arbitrary negative 0 10 0 0.1 ± 0.1
Randoms UTR alternate negative 2 10 0.2 0.1 ± 0.1
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 1 2 0.5 0.5 ± 0.5 (-+1,++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 1 10 0.1 0.1 ± 0
Randoms Proximal alternate negative 1 10 0.1 0.1 ± 0
Reals Proximal positive 0 2 0 0
Randoms Proximal arbitrary positive 0 10 0 0
Randoms Proximal alternate positive 0 10 0 0
Reals Distal negative 1 2 0.5 0.5 ± 0.5 (--0,+-1)
Randoms Distal arbitrary negative 5 10 0.5 0.45 ± 0.05
Randoms Distal alternate negative 4 10 0.4 0.45 ± 0.05
Reals Distal positive 2 2 1 1 ± 0 (-+1,++1)
Randoms Distal arbitrary positive 7 10 0.7 0.65 ± 0.05
Randoms Distal alternate positive 6 10 0.6 0.65 ± 0.05

Comparison:

The occurrences of real modified Prolamin box UTRs, cores, and distals are greater than the randoms. This suggests that the real modified Prolamin boxes are likely active or activable.

Natural prolamin box

A 7 bp element (TGTAAAG) termed the Prolamin Box (P-box).[1]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 1 2 0.5 0.5 ± 0.5 (--1,+-0)
Randoms UTR arbitrary negative 0 10 0 0.1 ± 0.1
Randoms UTR alternate negative 2 10 0.2 0.1 ± 0.1
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 1 10 0.1 0.05 ± 0.05
Randoms Proximal alternate negative 0 10 0 0.05 ± 0.05
Reals Proximal positive 0 2 0 0
Randoms Proximal arbitrary positive 0 10 0 0
Randoms Proximal alternate positive 0 10 0 0
Reals Distal negative 0 2 0 0
Randoms Distal arbitrary negative 1 10 0.1 0.15 ± 0.05
Randoms Distal alternate negative 2 10 0.2 0.15 ± 0.05
Reals Distal positive 0 2 0 0
Randoms Distal arbitrary positive 5 10 0.5 0.35 ± 0.15
Randoms Distal alternate positive 2 10 0.2 0.35 ± 0.15

Comparison:

The occurrences of real Prolamin box UTRs are greater than the randoms. This suggests that the real Prolamin boxes 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 1.4 Montaña Mena, Jesus Vicente-Carbajosa, Robert J. Schmidt and Pilar Carbonero (October 1998). "An endosperm-specific DOF protein from barley, highly conserved in wheat, binds to and activates transcription from the prolamin-box of a native B-hordein promoter in barley endosperm". The Plant Journal. 16 (1): 53–62. doi:10.1046/j.1365-313x.1998.00275.x. Retrieved 2017-02-19.
  2. ↑ Veronica Ruta, Chiara Longo, Andrea Lepri, Veronica De Angelis, Sara Occhigrossi, Paolo Costantino and Paola Vittorioso (8 February 2020). "The DOF Transcription Factors in Seed and Seedling Development". Plants. 9 (2): 218. doi:10.3390/plants9020218. Retrieved 7 January 2021.

External links


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