ABA-response element gene transcriptions

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Associate Editor(s)-in-Chief: Henry A. Hoff

"The key cis-elements in [non-yellow coloring 1] NYC1 promoter, namely, ABA-response element (ABRE) (ACGTG), ACGT, GCCcore (GCCGCC), and ethylene-inducible 3 [EIN3-Like1] (EIN3)/EIL1-binding sequence (T[TAG][GA]CGT[GA][TCA][TAG]), can be targeted by ABA insensitive 3 (ABI3), ABI5, and ABF2, 3, 4 in the ABA-signaling pathway [60,61]. GCCGCC and EIN3/EIL1-binding sequence (T[TAG][GA]CGT[GA][TCA][TAG]) are induced by ethylene-inducible TF and EIN3/EIL1 in the ethylene signaling pathway [61]. Therefore, ABA signaling is crucial for [chlorophyll] Chl b reductase activities to catalyze the Chl degradation, the first part of leaf senescence."[1]

Consensus sequences

Main article: Consensus sequence gene transcriptions

"The ABA responsive element (ABRE) is a key cis‐regulatory element in ABA signalling. However, its consensus sequence (ACGTG(G/T)C) is present in the promoters of only about 40% of ABA‐induced genes in rice aleurone cells, suggesting other ABREs may exist."[2]

"Many ABA‐inducible genes in various species contain a conserved cis‐regulatory ABA responsive element (ABRE) with the consensus sequence ACGTG(G/T)C (Hattori et al. 2002; Shen et al. 2004)."[2]

"The [novel ABRE] ABREN, [GATCGATC], had the highest average score and highest average sites in the 1 kb upstream of the start codon of the highly ABA‐induced genes in aleurone. The CGATCGAT motif [...] was identified by Bioprospector more times, but the average score and number of sites were lower. This sequence is almost identical to the ABREN but with a leading cytosine. The ABRE [ACGTGTCC] was the third highest scoring motif."[2]

Using the ABREN (GATCGATC), the CGATCGAT motif, and the ABRE (ACGTGTCC)[2] suggests a general consensus sequence of 5'-(A/C/G)(A/C/G)(A/G/T)(C/T)(C/G)(A/G/T)(A/C/T)(C/T)-3' which would allow 1944 combinations including the principal three variations. As the ABREN has the repeat pattern "GATC" and the CGATCGAT motif is similar with "CGAT", looking for the smaller GATCGAT may be more productive, while the ABRE as "ACGTGTCC" can be searched separately.

The more reduced consensus sequence 5'-GATCGAT-3' may be a better choice while the ABRE 5'-ACGTGTCC-3' could be examined separately.

Hypotheses

  1. A1BG has no ABA-response elements in either promoter.
  2. A1BG is not transcribed by an ABA-response element.
  3. ABA-response elements do not participate in the transcription of A1BG.

ABREN samplings

Copying 5'-CCGTCTCC-3' in "⌘F" yields two between ZSCAN22 and A1BG and none between ZNF497 and A1BG as can be found by the computer programs.

Copying 5'-CAGCCACC-3' in "⌘F" yields none between ZSCAN22 and A1BG and one between ZNF497 and A1BG as can be found by the computer programs.

The last two above could be combined as 5'-C(A/C)G(C/T)C(A/T)CC-3' as another possible consensus sequence.

Copying 5'-GATCGAT-3' in "⌘F" yields none between ZSCAN22 and A1BG and none between ZNF497 and A1BG as can be found by the computer programs.

Copying 5'-T[TAG][GA]CGT[GA][TCA][TAG]-3' is 5'-T(A/G/T)(A/G)CGT(A/G)(A/C/T)(A/G/T)-3'.

For the Basic programs testing consensus sequence 3'-GATCGAT-5' (starting with SuccessablesABA.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 SuccessablesABA--.bas, looking for 3'-GATCGAT-5', 0.
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesABA-+.bas, looking for 3'-GATCGAT-5', 0.
  3. positive strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesABA+-.bas, looking for 3'-GATCGAT-5', 0.
  4. positive strand in the positive direction (from ZNF497 to A1BG) is SuccessablesABA++.bas, looking for 3'-GATCGAT-5', 0.
  5. complement, negative strand, negative direction is SuccessablesABAc--.bas, looking for 3'-CTAGCTA-5', 0.
  6. complement, negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesABAc-+.bas, looking for 3'-CTAGCTA-5', 0.
  7. complement, positive strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesABAc+-.bas, looking for 3'-CTAGCTA-5', 0.
  8. complement, positive strand in the positive direction (from ZNF497 to A1BG) is SuccessablesABAc++.bas, looking for 3'-CTAGCTA-5', 0.
  9. inverse complement, negative strand, negative direction is SuccessablesABAci--.bas, looking for 3'-ATCGATC-5', 0.
  10. inverse complement, negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesABAci-+.bas, looking for 3'-ATCGATC-5', 0.
  11. inverse complement, positive strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesABAci+-.bas, looking for 3'-ATCGATC-5', 0.
  12. inverse complement, positive strand in the positive direction (from ZNF497 to A1BG) is SuccessablesABAci++.bas, looking for 3'-ATCGATC-5', 0.
  13. inverse negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesABAi--.bas, looking for 3'-TAGCTAG-5', 0.
  14. inverse negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesABAi-+.bas, looking for 3'-TAGCTAG-5', 0.
  15. inverse positive strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesABAi+-.bas, looking for 3'-TAGCTAG-5', 0.
  16. inverse positive strand in the positive direction (from ZNF497 to A1BG) is SuccessablesABAi++.bas, looking for 3'-TAGCTAG-5', 0.

ABRE samplings

Copying 5'-ACGTG-3' in "⌘F" yields eight between ZSCAN22 and A1BG and one between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence 3'-ACGTG(G/T)C-5' (starting with SuccessablesABA.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 SuccessablesABA--.bas, looking for 3'-ACGTG(G/T)C-5', 0.
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesABA-+.bas, looking for 3'-ACGTG(G/T)C-5', 0.
  3. positive strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesABA+-.bas, looking for 3'-ACGTG(G/T)C-5', 1, 3'-ACGTGGC-5', 4239.
  4. positive strand in the positive direction (from ZNF497 to A1BG) is SuccessablesABA++.bas, looking for 3'-ACGTG(G/T)C-5', 2, 3'-ACGTGTC-5', 1823, 3'-ACGTGGC-5', 4344.
  5. complement, negative strand, negative direction is SuccessablesABAc--.bas, looking for 3'-TGCAC(A/C)G-5', 1, 3'-TGCACCG-5', 4239.
  6. complement, negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesABAc-+.bas, looking for 3'-TGCAC(A/C)G-5', 2, 3'-TGCACAG-5', 1823, 3'-TGCACCG-5', 4344.
  7. complement, positive strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesABAc+-.bas, looking for 3'-TGCAC(A/C)G-5', 0.
  8. complement, positive strand in the positive direction (from ZNF497 to A1BG) is SuccessablesABAc++.bas, looking for 3'-TGCAC(A/C)G-5', 0.
  9. inverse complement, negative strand, negative direction is SuccessablesABAci--.bas, looking for 3'-G(A/C)CACGT-5', 1, 3'-GACACGT-5', 3429.
  10. inverse complement, negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesABAci-+.bas, looking for 3'-G(A/C)CACGT-5', 0.
  11. inverse complement, positive strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesABAci+-.bas, looking for 3'-G(A/C)CACGT-5', 0.
  12. inverse complement, positive strand in the positive direction (from ZNF497 to A1BG) is SuccessablesABAci++.bas, looking for 3'-G(A/C)CACGT-5', 1, 3'-GACACGT-5', 2960.
  13. inverse negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesABAi--.bas, looking for 3'-C(G/T)GTGCA-5', 0.
  14. inverse negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesABAi-+.bas, looking for 3'-C(G/T)GTGCA-5', 1, 3'-CTGTGCA-5', 2960.
  15. inverse positive strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesABAi+-.bas, looking for 3'-C(G/T)GTGCA-5', 1, 3'-CTGTGCA-5', 3429.
  16. inverse positive strand in the positive direction (from ZNF497 to A1BG) is SuccessablesABAi++.bas, looking for 3'-C(G/T)GTGCA-5', 0.

ABRE Core promoters

Main article: Core promoter gene transcriptions

Positive strand, positive direction: 5'-ACGTGGC-3' at 4344 and complement.

ABRE Proximal promoters

Main article: Proximal promoter gene transcriptions

Positive strand, negative direction: 5'-ACGTGGC-3' at 4239 and complement.

ABRE Distal promoters

Main article: Distal promoter gene transcriptions

Negative strand, negative direction: 5'-GACACGT-3' at 3429 and complement.

Positive strand, positive direction: 5'-GACACGT-3' at 2960, 5'-ACGTGTC-3' at 1823 and complements.

ACGTGTCC samplings

For the Basic programs testing consensus sequence 3'-ACGTGTCC-5' (starting with SuccessablesABA.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, negative direction is SuccessablesABA--.bas, looking for 3'-ACGTGTCC-5', 0.
  2. negative strand, positive direction is SuccessablesABA-+.bas, looking for 3'-ACGTGTCC-5', 0.
  3. positive strand, negative direction is SuccessablesABA+-.bas, looking for 3'-ACGTGTCC-5', 0.
  4. positive strand, positive direction is SuccessablesABA++.bas, looking for 3'-ACGTGTCC-5', 0.
  5. complement, negative strand, negative direction is SuccessablesABAc--.bas, looking for 3'-TGCACAGG-5', 0.
  6. complement, negative strand, positive direction is SuccessablesABAc-+.bas, looking for 3'-TGCACAGG-5', 0.
  7. complement, positive strand, negative direction is SuccessablesABAc+-.bas, looking for 3'-TGCACAGG-5', 0.
  8. complement, positive strand, positive direction is SuccessablesABAc++.bas, looking for 3'-TGCACAGG-5', 0.
  9. inverse complement, negative strand, negative direction is SuccessablesABAci--.bas, looking for 3'-GGACACGT-5', 0.
  10. inverse complement, negative strand, positive direction is SuccessablesABAci-+.bas, looking for 3'-GGACACGT-5', 0.
  11. inverse complement, positive strand, negative direction is SuccessablesABAci+-.bas, looking for 3'-GGACACGT-5', 0.
  12. inverse complement, positive strand, positive direction is SuccessablesABAci++.bas, looking for 3'-GGACACGT-5', 0.
  13. inverse negative strand, negative direction is SuccessablesABAi--.bas, looking for 3'-CCTGTGCA-5', 0.
  14. inverse negative strand, positive direction is SuccessablesABAi-+.bas, looking for 3'-CCTGTGCA-5', 0.
  15. inverse positive strand, negative direction is SuccessablesABAi+-.bas, looking for 3'-CCTGTGCA-5', 0.
  16. inverse positive strand, positive direction is SuccessablesABAi++.bas, looking for 3'-CCTGTGCA-5', 0.

Acknowledgements

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

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

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

Initial content for this page in some instances incorporates text from the United States National Library of Medicine.

See also

References

  1. ↑ Muhammad Asad Ullah Asad, Shamsu Ado Zakari, Qian Zhao, Lujian Zhou, Yu Ye and Fangmin Cheng (10 January 2019). "Abiotic Stresses Intervene with ABA Signaling to Induce Destructive Metabolic Pathways Leading to Death: Premature Leaf Senescence in Plants". International Journal of Molecular Sciences. 20 (2): 256–278. doi:10.3390/ijms20020256. PMID 30634648. Retrieved 27 August 2020.
  2. ↑ 2.0 2.1 2.2 2.3 Kenneth A. Watanabe, Arielle Homayouni, Lingkun Gu, Kuan‐Ying Huang, Tuan‐Hua David Ho, Qingxi J. Shen (18 June 2017). "Transcriptomic analysis of rice aleurone cells identified a novel abscisic acid response element". Plant, Cell & Environment. 40 (9): 2004–2016. doi:10.1111/pce.13006. Retrieved 5 October 2020.

External links

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