ACGT-containing element gene transcriptions: Difference between revisions

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|pmid=
|pmid=
|accessdate=19 April 2019 }}</ref>
|accessdate=19 April 2019 }}</ref>
==ABA-response elements==
{{main|ABA-response element 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."<ref name=Watanabe/>
"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)."<ref name=Watanabe/>
==A boxes==
{{main|A box gene transcriptions}}
Most bZIP proteins show high binding affinity for the ACGT motifs, which include [...] TACGTA (A box) [...].<ref name=Landschulz>{{ cite journal
| vauthors = Landschulz WH, Johnson PF, McKnight SL | title = The leucine zipper: a hypothetical structure common to a new class of DNA binding proteins | journal = Science | volume = 240 | issue = 4860 | pages = 1759–64 | date = June 1988 | pmid = 3289117
| doi = 10.1126/science.3289117 | bibcode = 1988Sci...240.1759L
| url = https://semanticscholar.org/paper/3a61c172ddfa79ce9f4909ca6bea2f6f40f7893e }}</ref><ref name=Zhang2014>{{ cite journal
| vauthors = Z G E, Zhang YP, Zhou JH, Wang L
| title = Mini review roles of the bZIP gene family in rice
| journal = Genetics and Molecular Research
| volume = 13
| issue = 2
| pages = 3025–36
| date = April 2014
| pmid = 24782137
| doi = 10.4238/2014.April.16.11 }}</ref><ref name=Nijhawan>{{ cite journal | vauthors = Nijhawan A, Jain M, Tyagi AK, Khurana JP
| title = Genomic survey and gene expression analysis of the basic leucine zipper transcription factor family in rice
| journal = Plant Physiology
| volume = 146
| issue = 2
| pages = 333–50
| date = February 2008
| pmid = 18065552
| doi = 10.1104/pp.107.112821 }}</ref>
==Phosphate starvation-response transcription factors==
{{main|Phosphate starvation-response transcription factor gene transcriptions}}
"The [palindromic E-box motif (CACGTG)] motif is bound by the transcription factor Pho4, [and has the] class of basic helix-loop-helix DNA binding domain and core recognition sequence (Zhou and O'Shea 2011)."<ref name=Rossi>{{ cite journal
|author=Matthew J. Rossi, William K.M. Lai and B. Franklin Pugh
|title=Genome-wide determinants of sequence-specific DNA binding of general regulatory factors
|journal=Genome Research
|date=21 March 2018
|volume=28
|issue=
|pages=497-508
|url=https://genome.cshlp.org/content/28/4/497.full
|arxiv=
|bibcode=
|doi=10.1101/gr.229518.117
|pmid=29563167
|accessdate=31 August 2020 }}</ref>
The upstream activating sequence (UAS) for Pho4p is 5'-CAC(A/G)T(T/G)-3' in the promoters of ''HIS4'' and ''PHO5'' regarding phosphate limitation with respect to regulation of the purine and histidine biosynthesis pathways [66].<ref name=Tang>{{ cite journal
|author=Hongting Tang, Yanling Wu, Jiliang Deng, Nanzhu Chen, Zhaohui Zheng, Yongjun Wei, Xiaozhou Luo, and Jay D. Keasling
|title=Promoter Architecture and Promoter Engineering in ''Saccharomyces cerevisiae''
|journal=Metabolites
|date=6 August 2020
|volume=10
|issue=8
|pages=320-39
|url=https://www.mdpi.com/2218-1989/10/8/320/pdf
|arxiv=
|bibcode=
|doi=10.3390/metabo10080320
|pmid=32781665
|accessdate=18 September 2020 }}</ref>


==Consensus sequences==
==Consensus sequences==

Revision as of 22:31, 15 October 2020

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

The "binding affinities of both bZIP proteins were similar to CREA/T (ATGACGTCAT), a CRE sequence with flanking adenine and thymine (A/T) at positions -4 and +4. [The] bZIP domains of both STF1 and HY5 have similar binding properties for recognizing ACGT-containing elements (ACEs). [Although] the G-box is a known target site for the HY5 protein, the C-box sequences are the preferred binding sites for both STF1 and HY5."[1]

"The combination of an [ACGT-containing element] ACE and a MRE confers light responsiveness to the CFI, F3H and FLS promoters."[2]

"Upstream from the transcriptional start site, several motifs were found [...]. A typical TATA box is located at -43. The CAAT consensus sequence cannot be found between -80 and -120; however, two sequence motifs (GCGCCC, GGGCAG), which are homologous to the consensus sequences for the Spl-binding site, GGGCGG (GC box) [19] were found around -114 and -570. The GC box has been found in promoters of many viral and cellular genes [20], and acts as a binding site of a protein, Spl, which is necessary for transcriptional activity. A pyrimidine box (CCTTT) and Box I (GCAGTG) which are part of the GA response complex [21] were found at -208 and -256. Two 8 bp sequences (CACGTCGC, CACGTAAC) which are similar to an ABA response element (ABRE, CACGTGGC) [22] were located at -308, -648 relative to the + 1 site. The core sequence of the ABA response element (ACGT) is the binding site for basic leucine zipper transcriptional factors or common plant regulatory factors (CPRFs) [23]."[3]

ABA-response elements

Main article: ABA-response element 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."[4]

"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)."[4]

A boxes

Main article: A box gene transcriptions

Most bZIP proteins show high binding affinity for the ACGT motifs, which include [...] TACGTA (A box) [...].[5][6][7]

Phosphate starvation-response transcription factors

Main article: Phosphate starvation-response transcription factor gene transcriptions

"The [palindromic E-box motif (CACGTG)] motif is bound by the transcription factor Pho4, [and has the] class of basic helix-loop-helix DNA binding domain and core recognition sequence (Zhou and O'Shea 2011)."[8]

The upstream activating sequence (UAS) for Pho4p is 5'-CAC(A/G)T(T/G)-3' in the promoters of HIS4 and PHO5 regarding phosphate limitation with respect to regulation of the purine and histidine biosynthesis pathways [66].[9]

Consensus sequences

"The ABRE contains the core sequence, ACGT, also known as the G‐box (Marcotte et al. 1989; Yamaguchi‐Shinozaki et al. 1990)."[4]

5'-ACGT-3'.[3]

The consensus sequence for the ACGT-containing elements (ACEs) is 5'-CACGT-3'.[2]

Hypotheses

  1. A1BG has no ACEs in either promoter.

Samplings

  1. ACGT elements, negative strand, negative direction: 24 between 150 and 4338 nts.
  2. ACGT elements, negative strand, positive direction: 2, 3'-ACGT-5' at 569, 3'-ACGT-5' at 3254.
  3. ACGT elements, positive strand, negative direction: 4, 3'-ACGT-5' at 342, 3'-ACGT-5' at 531, 3'-ACGT-5' at 1772, 3'-ACGT-5' at 4236.
  4. ACGT elements, positive strand, positive direction: 44 between 192 and 4341 nts.

ACGT-containing elements include these metal responsive elements:

  1. complement, negative strand, negative direction: 6 between 1348 and 4341 nts.
  2. complement, positive strand, negative direction: 6 between 549 and 3323 nts.
  3. inverse, negative strand, negative direction: 2, 3'-CTCACGT-5' at 1470, 3'-CACACGT-5' at 2863.
  4. inverse, positive strand, negative direction: 2, 3'-CACACGT-5' at 531, 3'-CTCACGT-5' at 1772.
  5. inverse, positive strand, positive direction: 6 between 546 and 3883 nts.

ACGT-containing elements include these cAMP response elements (CRE):

  1. negative strand in the negative direction (from ZSCAN22 to A1BG): 1, 3'-TGACGTCA-5' at 4317.

Acknowledgements

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

See also

References

  1. ↑ Young Hun Song, Cheol Min Yoo, An Pio Hong, Seong Hee Kim, Hee Jeong Jeong, Su Young Shin, Hye Jin Kim, Dae-Jin Yun, Chae Oh Lim, Jeong Dong Bahk, Sang Yeol Lee, Ron T. Nagao, Joe L. Key, and Jong Chan Hong (April 2008). "DNA-Binding Study Identifies C-Box and Hybrid C/G-Box or C/A-Box Motifs as High-Affinity Binding Sites for STF1 and LONG HYPOCOTYL5 Proteins" (PDF). Plant Physiology. 146 (4): 1862–1877. doi:10.1104/pp.107.113217. Retrieved 26 March 2019.
  2. ↑ 2.0 2.1 Ulrike Hartmann, Martin Sagasser, Frank Mehrtens, Ralf Stracke and Bernd Weisshaar (January 2005). "Differential combinatorial interactions of cis-acting elements recognized by R2R3-MYB, BZIP, and BHLH factors control light-responsive and tissue-specific activation of phenylpropanoid biosynthesis genes" (PDF). Plant Molecular Biology. 57 (2): 155–171. doi:10.1007/s11103-004-6910-0. Retrieved 10 November 2018.
  3. ↑ 3.0 3.1 Lingqiang Guan, Alexis N. Polidoros and John G. Scandalios (March 1996). "Isolation, characterization and expression of the maize Cat2 catalase gene" (PDF). Plant Molecular Biology. 30 (5): 913–24. doi:10.1007/BF00020803. Retrieved 19 April 2019.
  4. ↑ 4.0 4.1 4.2 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.
  5. ↑ Landschulz WH, Johnson PF, McKnight SL (June 1988). "The leucine zipper: a hypothetical structure common to a new class of DNA binding proteins". Science. 240 (4860): 1759–64. Bibcode:1988Sci...240.1759L. doi:10.1126/science.3289117. PMID 3289117.
  6. ↑ Z G E, Zhang YP, Zhou JH, Wang L (April 2014). "Mini review roles of the bZIP gene family in rice". Genetics and Molecular Research. 13 (2): 3025–36. doi:10.4238/2014.April.16.11. PMID 24782137. Vancouver style error: name (help)
  7. ↑ Nijhawan A, Jain M, Tyagi AK, Khurana JP (February 2008). "Genomic survey and gene expression analysis of the basic leucine zipper transcription factor family in rice". Plant Physiology. 146 (2): 333–50. doi:10.1104/pp.107.112821. PMID 18065552.
  8. ↑ Matthew J. Rossi, William K.M. Lai and B. Franklin Pugh (21 March 2018). "Genome-wide determinants of sequence-specific DNA binding of general regulatory factors". Genome Research. 28: 497–508. doi:10.1101/gr.229518.117. PMID 29563167. Retrieved 31 August 2020.
  9. ↑ Hongting Tang, Yanling Wu, Jiliang Deng, Nanzhu Chen, Zhaohui Zheng, Yongjun Wei, Xiaozhou Luo, and Jay D. Keasling (6 August 2020). "Promoter Architecture and Promoter Engineering in Saccharomyces cerevisiae". Metabolites. 10 (8): 320–39. doi:10.3390/metabo10080320. PMID 32781665 Check |pmid= value (help). Retrieved 18 September 2020.

External links

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