ABA-response element gene transcriptions: Difference between revisions

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Revision as of 19:50, 3 May 2023

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]

"The hypoxia response element (HRE) and estrogen response element (ERE) were located on −154 to −150 "ACGTG", and −94 to −80 "AGGTTATTGCCTCCT" on the transcript, respectively."[2]

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."[3]

"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)."[3]

"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."[3]

Using the ABREN (GATCGATC), the CGATCGAT motif, and the ABRE (ACGTGTCC)[3] 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.

UTR ABRE promoters

  1. Negative strand, negative direction: GACACGT at 3429.
  1. Positive strand, negative direction: ACGTGGC at 4239.

ABRE Core promoters

Main article: Core promoter gene transcriptions

Positive strand, positive direction: ACGTGGC at 4344.

ABRE Distal promoters

Main article: Distal promoter gene transcriptions

Positive strand, positive direction: GACACGT at 2960, ACGTGTC at 1823.

ABRE random dataset samplings

  1. ABREr0: 0.
  2. ABREr1: 0.
  3. ABREr2: 1, ACGTGTC at 1596.
  4. ABREr3: 1, ACGTGGC at 1439.
  5. ABREr4: 0.
  6. ABREr5: 0.
  7. ABREr6: 1, ACGTGTC at 2907.
  8. ABREr7: 1, ACGTGGC at 3536.
  9. ABREr8: 1, ACGTGTC at 916.
  10. ABREr9: 0.
  11. ABREr0ci: 0.
  12. ABREr1ci: 3, GACACGT at 3788, GCCACGT at 3298, GCCACGT at 191.
  13. ABREr2ci: 0.
  14. ABREr3ci: 2, GCCACGT at 4080, GCCACGT at 1482.
  15. ABREr4ci: 1, GACACGT at 2286.
  16. ABREr5ci: 0.
  17. ABREr6ci: 0.
  18. ABREr7ci: 1, GACACGT at 1391.
  19. ABREr8ci: 1, GCCACGT at 897.
  20. ABREr9ci: 1, GCCACGT at 874.

ABREr UTRs

Main article: UTR promoter gene transcriptions
  1. ABREr6: ACGTGTC at 2907.

ABREr proximal promoters

Main article: Proximal promoter gene transcriptions
  1. ABREr3ci: GCCACGT at 4080.

ABREr distal promoters

Main article: Distal promoter gene transcriptions
  1. ABREr2: ACGTGTC at 1596.
  2. ABREr8: ACGTGTC at 916.
  3. ABREr4ci: GACACGT at 2286.
  4. ABREr8ci: GCCACGT at 897.


  1. ABREr3: ACGTGGC at 1439.
  2. ABREr7: ACGTGGC at 3536.
  3. ABREr1ci: GACACGT at 3788, GCCACGT at 3298, GCCACGT at 191.
  4. ABREr3ci: GCCACGT at 1482.
  5. ABREr7ci: GACACGT at 1391.
  6. ABREr9ci: GCCACGT at 874.

ABRE analysis and results

Main article: Complex locus A1BG and ZNF497 § Abscissic acid (ABA) response elements

"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."[3]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 2 2 1.0 1.0
Randoms UTR arbitrary negative 1 10 0.1 0.25
Randoms UTR alternate negative 4 10 0.4 0.25
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
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
Randoms Proximal alternate negative 0 10 0 0
Reals Proximal positive 0 2 0 0
Randoms Proximal arbitrary positive 1 10 0.1 0.05
Randoms Proximal alternate positive 0 10 0 0.05
Reals Distal negative 0 2 0 0
Randoms Distal arbitrary negative 4 10 0.4 0.45
Randoms Distal alternate negative 5 10 0.5 0.45
Reals Distal positive 2 2 1 1
Randoms Distal arbitrary positive 8 10 0.8 0.65
Randoms Distal alternate positive 5 10 0.5 0.65

Comparison:

The occurrences of real UTR and core ABREs are greater than the randoms. The occurrences for the real positive distals are greater than the randoms. This suggests that the real responsive element consensus sequences are likely active or activable with the possible exception of the real negative direction distal.

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.

Discussion

Abscissic acid (ABA) response elements (ABREs) have been identified for example in the UTR for A1BG between ZSCAN22 and A1BG. If these response elements are active then A1BG can be transcribed as a key cis-regulatory element in ABA signaling. "However, for ABA responsive transcription to occur, a single copy of the ABRE is not sufficient. In barley, the combination of an ABRE and one of two known coupling elements CE1 (TGCCACCGG) and CE3 (GCGTGTC) constitutes an ABA responsive complex (ABRC) in the regulation of the ABA‐inducible genes HVA1 and HVA22 (Shen and Ho 1995; Shen et al. 1996). It was also shown that a pair of ABREs can function as an ABRC with the second ABRE playing the role of the coupling element in rice (Hobo et al. 1999), barley (Shen et al. 1996) and Arabidopsis (Nakashima et al. 2006). Coupling of two CE3s is much less active in conferring ABA response to the minimal promoter (Shen et al. 2004). Interestingly, CE3 appears to be specific to monocots. In Arabidopsis, the CE3 element is practically absent; thus, Arabidopsis relies on paired ABREs to form ABRCs (Gomez‐Porras et al. 2007) or on the coupling of a DRE (TACCGACAT) with ABRE (Narusaka et al. 2003; Nakashima et al. 2006)."[3]

No coupling elements occur in the negative direction between ZSCAN22 and A1BG. Two ABREs occur in both directions suggesting pairs may be available to function as an ABRC on either side of A1BG, subject to needed proximity. The random datasets have more occurrences further away from A1BG and always much fewer occurrences per dataset. These suggest that those around A1BG are not random and are likely active or activatable.

No DRE (TACCGACAT) occurs in either direction of A1BG.

Testing on Google Scholar: A1BG "ABA responsive element" - did not match any articles. Testing: A1BG ABRE produced 6 articles but ABRE in the first was not Abscissic acid (ABA) response element (ABRE). One other contained the Spanish word abre. The only ABRE found in the promoters of A1BG is ACGTG(G/T)C (Watanabe) with four occurrences. Coupling element (CE1) is absent but CE3 is present as GCGTGTC (Watanabe) and CACGCG (Ding). The DREB box or (CRT/DREB box) are absent.

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. ↑ Takuya Matsumoto, Saemi Kitajima, Chisato Yamamoto, Mitsuru Aoyagi, Yoshiharu Mitoma, Hiroyuki Harada and Yuji Nagashima (9 August 2020). "Cloning and tissue distribution of the ATP-binding cassette subfamily G member 2 gene in the marine pufferfish Takifugu rubripes" (PDF). Fisheries Science. 86: 873–887. doi:10.1007/s12562-020-01451-z. Retrieved 27 September 2020.
  3. ↑ 3.0 3.1 3.2 3.3 3.4 3.5 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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