Adr1p gene transcriptions: Difference between revisions

Revision as of 00:51, 15 September 2021

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

"Saccharomyces cerevisiae Alcohol dehydrogenase repressor 1 (Adr1p, YDR216W) is the transcription activator of the ADH2 gene (alcohol dehydrogenase 2) [1,2], which participates in the metabolic switch from glucose to ethanol or glycerol as food sources in yeast. Adr1p is involved in the activation of a number of genes of the respiratory metabolism, including those that regulate peroxisomes and phospholipid biosynthesis [3,4]."^[1]

"ADR1 encodes a transcription factor that is a member of the C2H2 zinc finger class. Adr1p binds to promoters as a monomer in the absence of glucose to activate transcription of genes required for utilization of non-glucose carbon sources. Its targets include genes involved in catabolism of nonfermentable carbon sources such as ethanol, glycerol, and lactate (e.g., ADH2, ACS1, and GUT1), and also genes involved in peroxisome biogenesis and fatty acid utilization (e.g., POX1 and PXA1). In addition, binding of Adr1p to subtelomeric sites may affect the boundaries of silenced regions. Adr1p is part of the regulatory network controlling glucose repression and its alleviation in the absence of glucose, and as such, its expression and activity are tightly regulated by multiple glucose-response signals."^[2]

Consensus sequences

The upstream activating sequence (UAS) for Adr1p is 5'-TTGGGG-3' or 5'-TTGG(A/G)G-3'.^[3]

Samplings

Copying 5'-TTGGGG-3' in "⌘F" yields six 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 5'-TTGG(A/G)G-3' (starting with SuccessablesADR.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:

negative strand, negative direction, looking for 5'-TTGG(A/G)G-3', 7, 5'-TTGGAG-3' at 3786, 5'-TTGGGG-3' at 3150, 5'-TTGGGG-3' at 2623, 5'-TTGGGG-3' at 2286, 5'-TTGGGG-3' at 1859, 5'-TTGGGG-3' at 1216, 5'-TTGGGG-3' at 616, and complements.
negative strand, positive direction, looking for 5'-TTGG(A/G)G-3', 2, 5'-TTGGGG-3' at 4302, 5'-TTGGGG-3' at 2285, and complements.
positive strand, negative direction, looking for 5'-TTGG(A/G)G-3', 2, 5'-TTGGAG-3' at 3118, 5'-TTGGGG-3' at 2923, and complements.
positive strand, positive direction, looking for 5'-TTGG(A/G)G-3', 3, 5'-TTGGGG-3' at 3939, 5'-TTGGAG-3' at 1618, 5'-TTGGAG-3' at 610, and complements.
complement, negative strand, negative direction, looking for 5'-AACC(C/T)C-3', 2, 5'-AACCTC-3' at 3118, 5'-AACCCC-3' at 2923, and complements.
complement, negative strand, positive direction, looking for 5'-AACC(C/T)C-3', 3, 5'-AACCCC-3' at 3939, 5'-AACCTC-3' at 1618, 5'-AACCTC-3' at 610, and complements.
complement, positive strand, negative direction, looking for 5'-AACC(C/T)C-3', 7, 5'-AACCTC-3' at 3786, 5'-AACCCC-3' at 3150, 5'-AACCCC-3' at 2623, 5'-AACCCC-3' at 2286, 5'-AACCCC-3' at 1859, 5'-AACCCC-3' at 1216, 5'-AACCCC-3' at 616, and complements.
complement, positive strand, positive direction, looking for 5'-AACC(C/T)C-3', 2, 5'-AACCCC-3' at 4302, 5'-AACCCC-3' at 2285, and complements.
inverse complement, negative strand, negative direction, looking for 5'-C(C/T)CCAA-3', 6, 5'-CCCCAA-3' at 3803, 5'-CTCCAA-3' at 3260, 5'-CTCCAA-3' at 2397, 5'-CTCCAA-3' at 1318, 5'-CTCCAA-3' at 1027, 5'-CTCCAA-3' at 861, and complements.
inverse complement, negative strand, positive direction, looking for 5'-C(C/T)CCAA-3', 5, 5'-CTCCAA-3' at 1278, 5'-CTCCAA-3' at 942, 5'-CTCCAA-3' at 842, 5'-CTCCAA-3' at 606, 5'-CCCCAA-3' at 176, and complements.
inverse complement, positive strand, negative direction, looking for 5'-C(C/T)CCAA-3', 0.
inverse complement, positive strand, positive direction, looking for 5'-C(C/T)CCAA-3', 2, 5'-CTCCAA-3' at 1925, 5'-CTCCAA-3' at 304.
inverse negative strand, negative direction, looking for 5'-G(A/G)GGTT-3', 0.
inverse negative strand, positive direction, looking for 5'-G(A/G)GGTT-3', 2, 5'-GAGGTT-3' at 1925, 5'-GAGGTT-3' at 304, and complements.
inverse positive strand, negative direction, looking for 5'-G(A/G)GGTT-3', 6, 5'-GGGGTT-3' at 3803, 5'-GAGGTT-3' at 3260, 5'-GAGGTT-3' at 2397, 5'-GAGGTT-3' at 1318, 5'-GAGGTT-3' at 1027, 5'-GAGGTT-3' at 861, and complements.
inverse positive strand, positive direction, looking for 5'-G(A/G)GGTT-3', 5, 5'-GAGGTT-3' at 1278, 5'-GAGGTT-3' at 942, 5'-GAGGTT-3' at 842, 5'-GAGGTT-3' at 606, 5'-GGGGTT-3' at 176, and complements.

ADR core promoters

Negative strand, positive direction: 5'-TTGGGG-3' at 4302, and complement.

ADR proximal promoters

ADR distal promoters

Negative strand, negative direction: 5'-CCCCAA-3' at 3803, 5'-TTGGAG-3' at 3786, 5'-CTCCAA-3' at 3260, 5'-TTGGGG-3' at 3150, 5'-AACCTC-3' at 3118, 5'-AACCCC-3' at 2923, 5'-TTGGGG-3' at 2623, 5'-CTCCAA-3' at 2397, 5'-TTGGGG-3' at 2286, 5'-TTGGGG-3' at 1859, 5'-CTCCAA-3' at 1318, 5'-TTGGGG-3' at 1216, 5'-CTCCAA-3' at 1027, 5'-CTCCAA-3' at 861, 5'-TTGGGG-3' at 616, and complements.

Positive strand, negative direction: 5'-TTGGAG-3' at 3118, 5'-TTGGGG-3' at 2923, and complements.

Negative strand, positive direction: 5'-TTGGGG-3' at 2285, 5'-CTCCAA-3' at 1278, 5'-CTCCAA-3' at 942, 5'-CTCCAA-3' at 842, 5'-CTCCAA-3' at 606, 5'-CCCCAA-3' at 176, and complements.

Positive strand, positive direction: 5'-TTGGGG-3' at 3939, 5'-CTCCAA-3' at 1925, 5'-TTGGAG-3' at 1618, 5'-TTGGAG-3' at 610, 5'-CTCCAA-3' at 304, and complements.

Acknowledgements

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

References

↑ Memmo Buttinelli, Gianna Panetta, Ambra Bucci, Daniele Frascaria, Veronica Morea and Adriana Erica Miele (17 September 2019). "Protein Engineering of Multi-Modular Transcription Factor Alcohol Dehydrogenase Repressor 1 (Adr1p), a Tool for Dissecting In Vitro Transcription Activation". Biomolecules. 9 (9): 497. doi:10.3390/biom9090497. Retrieved 30 October 2020.
↑ Hlynialuk C, Schierholtz R, Vernooy A, van der Merwe G (2008). "ADR1 / YDR216W Regulation". YeastGenome. Retrieved 14 September 2021.
↑ 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

[Buttinelli-1] Memmo Buttinelli, Gianna Panetta, Ambra Bucci, Daniele Frascaria, Veronica Morea and Adriana Erica Miele (17 September 2019). "Protein Engineering of Multi-Modular Transcription Factor Alcohol Dehydrogenase Repressor 1 (Adr1p), a Tool for Dissecting In Vitro Transcription Activation". Biomolecules. 9 (9): 497. doi:10.3390/biom9090497. Retrieved 30 October 2020.

[Hlynialuk-2] Hlynialuk C, Schierholtz R, Vernooy A, van der Merwe G (2008). "ADR1 / YDR216W Regulation". YeastGenome. Retrieved 14 September 2021.

[Tang-3] 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.

[1]

[2]

[3]

@@ Line 15: / Line 15: @@
 |pmid=
 |accessdate=30 October 2020 }}</ref>
+"ADR1 encodes a transcription factor that is a member of the C2H2 zinc finger class. Adr1p binds to promoters as a monomer in the absence of glucose to activate transcription of genes required for utilization of non-glucose carbon sources. Its targets include genes involved in catabolism of nonfermentable carbon sources such as ethanol, glycerol, and lactate (e.g., ADH2, ACS1, and GUT1), and also genes involved in peroxisome biogenesis and fatty acid utilization (e.g., POX1 and PXA1). In addition, binding of Adr1p to subtelomeric sites may affect the boundaries of silenced regions. Adr1p is part of the regulatory network controlling glucose repression and its alleviation in the absence of glucose, and as such, its expression and activity are tightly regulated by multiple glucose-response signals."<ref name=Hlynialuk>{{ cite web
+|author=Hlynialuk C, Schierholtz R, Vernooy A, van der Merwe G
+|title=ADR1 / YDR216W Regulation
+|publisher=YeastGenome
+|location=
+|date=2008
+|url=https://www.yeastgenome.org/locus/Adr1/regulation
+|accessdate=14 September 2021 }}</ref>
 ==Consensus sequences==

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transcriptions MYB recognition element gene transcriptions Myelocytomatosis transcription factor gene transcriptions Myocyte enhancer factor gene transcriptions N-boxes Ndt80p gene transcriptions Nuclear factor 1 Nuclear factor 𝜿B Nuclear factor gene transcriptions Nuclear factor of activated T cell gene transcriptions (NFAT) Nuclear factor Y gene transcriptions Nutrient-sensing response element gene transcriptions Oaf1p gene transcriptions ORE1 binding site gene transcriptions p53 response element gene transcriptions P63 DNA-binding site gene transcriptions P box gene transcriptions Pdr1,3p gene transcriptions Peroxisome proliferator hormone response element gene transcriptions Phosphate starvation-response transcription factor gene transcriptions Pollen1 element gene transcriptions Polycomb response element gene transcriptions Preinitiation complex Preinitiation complex gene transcriptions Pribnow box gene transcriptions Prolamin box gene transcriptions Promoter gene transcriptions 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transcriptions Transcription factor 3 gene transcriptions Transcription factory gene transcriptions Transcription start site gene transcriptions Translational control sequence gene transcriptions U box gene transcriptions Unfolded protein response element gene transcriptions Upstream response element gene transcriptions Upstream stimulatory factor gene transcriptions UTR promoter gene transcriptions V and P box gene transcriptions V box gene transcriptions Vhr1p gene transcriptions Vitamin D response element gene transcriptions W box gene transcriptions X box gene transcriptions Xbp1p gene transcriptions X core promoter element gene transcriptions Xenobiotic response element gene transcriptions Xenobiotic responsive element gene transcriptions Yap1p,2p gene transcriptions Y box gene transcriptions YY1 gene transcriptions Zap1p gene transcriptions Z box gene transcriptions Zinc responsive element gene transcriptions