Adr1p gene transcriptions: Difference between revisions

Revision as of 19:47, 14 October 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]

ADR samplings

Copying TTGGGG 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 TTGG(A/G)G (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 TTGG(A/G)G, 7, TTGGAG at 3786, TTGGGG at 3150, TTGGGG at 2623, TTGGGG at 2286, TTGGGG at 1859, TTGGGG at 1216, TTGGGG at 616, and complements.
negative strand, positive direction, looking for TTGG(A/G)G, 2, TTGGGG at 4302, TTGGGG at 2285, and complements.
positive strand, negative direction, looking for TTGG(A/G)G, 2, TTGGAG at 3118, TTGGGG at 2923, and complements.
positive strand, positive direction, looking for TTGG(A/G)G, 3, TTGGGG at 3939, TTGGAG at 1618, TTGGAG at 610, and complements.
inverse complement, negative strand, negative direction, looking for C(C/T)CCAA, 6, CCCCAA at 3803, CTCCAA at 3260, CTCCAA at 2397, CTCCAA at 1318, CTCCAA at 1027, CTCCAA at 861, and complements.
inverse complement, negative strand, positive direction, looking for C(C/T)CCAA, 5, CTCCAA at 1278, CTCCAA at 942, CTCCAA at 842, CTCCAA at 606, CCCCAA at 176, and complements.
inverse complement, positive strand, negative direction, looking for C(C/T)CCAA, 0.
inverse complement, positive strand, positive direction, looking for C(C/T)CCAA, 2, CTCCAA at 1925, CTCCAA at 304.

ADR core promoters

Negative strand, positive direction: TTGGGG at 4302, and complement.

ADR distal promoters

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

Positive strand, negative direction: TTGGAG at 3118, TTGGGG at 2923, and complements.

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

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

ADR random dataset samplings

ADRr0: 1, TTGGGG at 1646.
ADRr1: 3, TTGGAG at 4179, TTGGGG at 2942, TTGGGG at 2008.
ADRr2: 8, TTGGGG at 4439, TTGGGG at 3047, TTGGAG at 2998, TTGGAG at 2258, TTGGAG at 1066, TTGGAG at 1032, TTGGGG at 624, TTGGGG at 214.
RDr3: 0.
RDr4: 0.
RDr5: 0.
RDr6: 0.
RDr7: 0.
RDr8: 0.
RDr9: 0.
RDr0ci: 0.
RDr1ci: 0.
RDr2ci: 0.
RDr3ci: 0.
RDr4ci: 0.
RDr5ci: 0.
RDr6ci: 0.
RDr7ci: 0.
RDr8ci: 0.
RDr9ci: 0.

RDr UTRs

RDr core promoters

RDr proximal promoters

RDr distal promoters

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 74: / Line 74: @@
 # ADRr0: 1, TTGGGG at 1646.
 # ADRr1: 3, TTGGAG at 4179, TTGGGG at 2942, TTGGGG at 2008.
-# RDr2: 0.
+# ADRr2: 8, TTGGGG at 4439, TTGGGG at 3047, TTGGAG at 2998, TTGGAG at 2258, TTGGAG at 1066, TTGGAG at 1032, TTGGGG at 624, TTGGGG at 214.
 # RDr3: 0.
 # RDr4: 0.

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