Adr1p gene transcriptions

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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

Main article: Consensus sequence gene transcriptions

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:

  1. 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.
  2. Negative strand, positive direction, looking for TTGG(A/G)G, 2, TTGGGG at 4302, TTGGGG at 2285.
  3. Positive strand, negative direction, looking for TTGG(A/G)G, 2, TTGGAG at 3118, TTGGGG at 2923.
  4. Positive strand, positive direction, looking for TTGG(A/G)G, 3, TTGGGG at 3939, TTGGAG at 1618, TTGGAG at 610.
  5. 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.
  6. 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.
  7. inverse complement, positive strand, negative direction, looking for C(C/T)CCAA, 0.
  8. inverse complement, positive strand, positive direction, looking for C(C/T)CCAA, 2, CTCCAA at 1925, CTCCAA at 304.

ADR (4560-2846) UTRs

  1. Negative strand, negative direction: CCCCAA at 3803, TTGGAG at 3786, CTCCAA at 3260, TTGGGG at 3150.
  2. Positive strand, negative direction: TTGGAG at 3118, TTGGGG at 2923.

ADR positive direction (4445-4265) core promoters

  1. Negative strand, positive direction: TTGGGG at 4302.

ADR negative direction (2811-2596) proximal promoters

  1. Negative strand, negative direction: TTGGGG at 2623.

ADR negative direction (2596-1) distal promoters

  1. Negative strand, negative direction: CTCCAA at 2397, TTGGGG at 2286, TTGGGG at 1859, CTCCAA at 1318, TTGGGG at 1216, CTCCAA at 1027, CTCCAA at 861, TTGGGG at 616.

ADR positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: TTGGGG at 2285, CTCCAA at 1278, CTCCAA at 942, CTCCAA at 842, CTCCAA at 606, CCCCAA at 176.
  2. Positive strand, positive direction: TTGGGG at 3939, CTCCAA at 1925, TTGGAG at 1618, TTGGAG at 610, CTCCAA at 304.

ADR random dataset samplings

  1. ADRr0: 1, TTGGGG at 1646.
  2. ADRr1: 3, TTGGAG at 4179, TTGGGG at 2942, TTGGGG at 2008.
  3. 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.
  4. ADRr3: 8, TTGGGG at 4354, TTGGGG at 3634, TTGGAG at 2828, TTGGAG at 2189, TTGGGG at 2111, TTGGAG at 1918, TTGGAG at 737, TTGGAG at 184.
  5. ADRr4: 5, TTGGGG at 4105, TTGGAG at 3578, TTGGGG at 3099, TTGGGG at 2839, TTGGAG at 2578.
  6. ADRr5: 5, TTGGAG at 3604, TTGGGG at 3000, TTGGAG at 2434, TTGGAG at 2300, TTGGGG at 44.
  7. ADRr6: 4, TTGGAG at 4101, TTGGGG at 3929, TTGGGG at 3274, TTGGAG at 1028.
  8. ADRr7: 5, TTGGGG at 3973, TTGGGG at 3164, TTGGAG at 2526, TTGGGG at 1850, TTGGGG at 856.
  9. ADRr8: 3, TTGGGG at 2455, TTGGGG at 2198, TTGGGG at 857.
  10. ADRr9: 4, TTGGGG at 3052, TTGGAG at 2978, TTGGAG at 2566, TTGGAG at 1451.
  11. ADRr0ci: 2, CCCCAA at 2613, CTCCAA at 1293.
  12. ADRr1ci: 3, CCCCAA at 4512, CTCCAA at 518, CTCCAA at 70.
  13. ADRr2ci: 6, CCCCAA at 4079, CCCCAA at 3881, CTCCAA at 3390, CCCCAA at 2566, CCCCAA at 1353, CTCCAA at 1319.
  14. ADRr3ci: 5, CCCCAA at 4251, CCCCAA at 3302, CTCCAA at 1904, CCCCAA at 235, CCCCAA at 155.
  15. ADRr4ci: 3, CCCCAA at 3564, CCCCAA at 2479, CTCCAA at 416.
  16. ADRr5ci: 3, CCCCAA at 1636, CCCCAA at 1614, CTCCAA at 910.
  17. ADRr6ci: 5, CCCCAA at 3524, CCCCAA at 3036, CCCCAA at 2958, CTCCAA at 1089, CCCCAA at 1035.
  18. ADRr7ci: 3, CTCCAA at 3031, CTCCAA at 951, CCCCAA at 273.
  19. ADRr8ci: 1, CTCCAA at 2218.
  20. ADRr9ci: 4, CCCCAA at 4399, CCCCAA at 3138, CCCCAA at 2074, CCCCAA at 1915.

ADRr arbitrary (evens) (4560-2846) UTRs

  1. ADRr2: TTGGGG at 4439, TTGGGG at 3047, TTGGAG at 2998.
  2. ADRr4: TTGGGG at 4105, TTGGAG at 3578, TTGGGG at 3099.
  3. ADRr6: TTGGAG at 4101, TTGGGG at 3929, TTGGGG at 3274.
  4. ADRr2ci: CCCCAA at 4079, CCCCAA at 3881, CTCCAA at 3390.
  5. ADRr4ci: CCCCAA at 3564.
  6. ADRr6ci: CCCCAA at 3524, CCCCAA at 3036, CCCCAA at 2958.

ADRr alternate (odds) (4560-2846) UTRs

  1. ADRr1: TTGGAG at 4179, TTGGGG at 2942.
  2. ADRr3: TTGGGG at 4354, TTGGGG at 3634.
  3. ADRr5: TTGGAG at 3604, TTGGGG at 3000.
  4. ADRr7: TTGGGG at 3973, TTGGGG at 3164.
  5. ADRr9: TTGGGG at 3052, TTGGAG at 2978.
  6. ADRr1ci: CCCCAA at 4512.
  7. ADRr3ci: CCCCAA at 4251, CCCCAA at 3302.
  8. ADRr7ci: CTCCAA at 3031.
  9. ADRr9ci: CCCCAA at 4399, CCCCAA at 3138.

ADRr arbitrary negative direction (evens) (2846-2811) core promoters

  1. ADRr4: TTGGGG at 2839.

ADRr alternate negative direction (odds) (2846-2811) core promoters

  1. ADRr3: TTGGAG at 2828.

ADRr arbitrary positive direction (odds) (4445-4265) core promoters

  1. ADRr3: TTGGGG at 4354.
  2. ADRr9ci: CCCCAA at 4399.

ADRr alternate positive direction (evens) (4445-4265) core promoters

  1. ADRr2: TTGGGG at 4439.

ADRr arbitrary negative direction (evens) (2811-2596) proximal promoters

  1. ADRr0ci: CCCCAA at 2613.

ADRr arbitrary positive direction (odds) (4265-4050) proximal promoters

  1. ADRr1: TTGGAG at 4179.

ADRr alternate positive direction (evens) (4265-4050) proximal promoters

  1. ADRr4: TTGGGG at 4105.
  2. ADRr6: TTGGAG at 4101.
  3. ADRr2ci: CCCCAA at 4079.

ADRr arbitrary negative direction (evens) (2596-1) distal promoters

  1. ADRr0: TTGGGG at 1646.
  2. ADRr2: TTGGAG at 2258, TTGGAG at 1066, TTGGAG at 1032, TTGGGG at 624, TTGGGG at 214.
  3. ADRr4: TTGGAG at 2578.
  4. ADRr6: TTGGAG at 1028.
  5. ADRr8: TTGGGG at 2455, TTGGGG at 2198, TTGGGG at 857.
  6. ADRr0ci: CTCCAA at 1293.
  7. ADRr2ci: CCCCAA at 2566, CCCCAA at 1353, CTCCAA at 1319.
  8. ADRr4ci: CCCCAA at 2479, CTCCAA at 416.
  9. ADRr6ci: CTCCAA at 1089, CCCCAA at 1035.
  10. ADRr8ci: CTCCAA at 2218.

ADRr alternate negative direction (odds) (2596-1) distal promoters

  1. ADRr1: TTGGGG at 2008.
  2. ADRr3: TTGGAG at 2189, TTGGGG at 2111, TTGGAG at 1918, TTGGAG at 737, TTGGAG at 184.
  3. ADRr5: TTGGAG at 2434, TTGGAG at 2300, TTGGGG at 44.
  4. ADRr7: TTGGAG at 2526, TTGGGG at 1850, TTGGGG at 856.
  5. ADRr9: TTGGAG at 2566, TTGGAG at 1451.
  6. ADRr5ci: CCCCAA at 1636, CCCCAA at 1614, CTCCAA at 910.
  7. ADRr7ci: CTCCAA at 951, CCCCAA at 273.
  8. ADRr9ci: CCCCAA at 2074, CCCCAA at 1915.

ADRr arbitrary positive direction (odds) (4050-1) distal promoters

  1. ADRr1: TTGGGG at 2942, TTGGGG at 2008.
  2. ADRr3: TTGGGG at 3634, TTGGAG at 2828, TTGGAG at 2189, TTGGGG at 2111, TTGGAG at 1918, TTGGAG at 737, TTGGAG at 184.
  3. ADRr5: TTGGAG at 3604, TTGGGG at 3000, TTGGAG at 2434, TTGGAG at 2300, TTGGGG at 44.
  4. ADRr7: TTGGGG at 3973, TTGGGG at 3164, TTGGAG at 2526, TTGGGG at 1850, TTGGGG at 856.
  5. ADRr9: TTGGGG at 3052, TTGGAG at 2978, TTGGAG at 2566, TTGGAG at 1451.
  6. ADRr1ci: CTCCAA at 518, CTCCAA at 70.
  7. ADRr3ci:CCCCAA at 3302, CTCCAA at 1904, CCCCAA at 235, CCCCAA at 155.
  8. ADRr5ci: CCCCAA at 1636, CCCCAA at 1614, CTCCAA at 910.
  9. ADRr7ci: CTCCAA at 3031, CTCCAA at 951, CCCCAA at 273.
  10. ADRr9ci: CCCCAA at 3138, CCCCAA at 2074, CCCCAA at 1915.

ADRr alternate positive direction (evens) (4050-1) distal promoters

  1. ADRr0: TTGGGG at 1646.
  2. ADRr2: TTGGGG at 3047, TTGGAG at 2998, TTGGAG at 2258, TTGGAG at 1066, TTGGAG at 1032, TTGGGG at 624, TTGGGG at 214.
  3. ADRr4: TTGGAG at 3578, TTGGGG at 3099, TTGGGG at 2839, TTGGAG at 2578.
  4. ADRr6: TTGGGG at 3929, TTGGGG at 3274, TTGGAG at 1028.
  5. ADRr8: TTGGGG at 2455, TTGGGG at 2198, TTGGGG at 857.
  6. ADRr0ci: CCCCAA at 2613, CTCCAA at 1293.
  7. ADRr2ci: CCCCAA at 3881, CTCCAA at 3390, CCCCAA at 2566, CCCCAA at 1353, CTCCAA at 1319.
  8. ADRr4ci: CCCCAA at 3564, CCCCAA at 2479, CTCCAA at 416.
  9. ADRr6ci: CCCCAA at 3524, CCCCAA at 3036, CCCCAA at 2958, CTCCAA at 1089, CCCCAA at 1035.
  10. ADRr8ci: CTCCAA at 2218.

ADR analysis and results

Main article: Complex locus A1BG and ZNF497 § Alcohol dehydrogenase repressor 1

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

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 6 2 3 3
Randoms UTR arbitrary negative 16 10 1.6 1.6
Randoms UTR alternate negative 16 10 1.6 1.6
Reals Core negative 0 2 0 0
Randoms Core arbitrary negative 1 10 0.1 0.1
Randoms Core alternate negative 1 10 0.1 0.1
Reals Core positive 1 2 0.5 0.5
Randoms Core arbitrary positive 2 10 0.2 0.15
Randoms Core alternate positive 1 10 0.1 0.15
Reals Proximal negative 1 2 0.5 0.5
Randoms Proximal arbitrary negative 1 10 0.1 0.05
Randoms Proximal alternate negative 0 10 0 0.05
Reals Proximal positive 0 2 0 0
Randoms Proximal arbitrary positive 1 10 0.1 0.2
Randoms Proximal alternate positive 3 10 0.3 0.2
Reals Distal negative 8 2 4 4
Randoms Distal arbitrary negative 20 10 2.0 2.05
Randoms Distal alternate negative 21 10 2.1 2.05
Reals Distal positive 11 2 5.5 5.5
Randoms Distal arbitrary positive 38 10 3.8 3.6
Randoms Distal alternate positive 34 10 3.4 3.6

Comparison:

The occurrences of real ADR UTRs, positive direction cores, negative direction proximals, and distals are greater than the randoms. This suggests that the real ADRs are likely active or activable.

Acknowledgements

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

See also

References

  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.
  2. ↑ Hlynialuk C, Schierholtz R, Vernooy A, van der Merwe G (2008). "ADR1 / YDR216W Regulation". YeastGenome. Retrieved 14 September 2021.
  3. ↑ 3.0 3.1 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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