Yap1p,2p gene transcriptions

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

"The activity of the native TRX2 promoter, which is regulated by the transcription factor Yap1p, can be altered by sensing NADPH/NADP+ ratios, but its sensitivity is low. Increasing the number of the UAS-containing Yap1p binding sites greatly enhanced the cascade response effect, and this novel biosensor was useful at selecting cell populations with higher NADPH/NADP+ ratios [139]."[1]

"Saccharomyces cerevisiae contains eight members of a novel and fungus-specific family of bZIP proteins that is defined by four atypical residues on the DNA-binding surface. Two of these proteins, Yap1 and Yap2, are transcriptional activators involved in pleiotropic drug resistance. Although initially described as AP-1 factors, at least four Yap proteins bind most efficiently to TTACTAA, a sequence that differs at position ±2 from the optimal AP-1 site (TGACTCA); further, a Yap-like derivative of the AP-1 factor Gcn4 (A239Q S242F) binds efficiently to the Yap recognition sequence."[2]

Human genes

Main article: Human genes

Interactions

Main article: Interaction gene transcriptions

Consensus sequences

Main article: Consensus sequence gene transcriptions

The upstream activating sequence (UAS) for Yap1p/2p is TTACTAA, which is found in genes GSH1, TRX2, YCF1, GLR1, induced by oxidative stress such as H2O2, for regulation of genes expressed in response to environmental changes.[1]

Yap samplings

Main article: Model samplings

Copying TTACTAA in "⌘F" yields none between ZSCAN22 and A1BG and none between ZNF497 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence TTACTAA (starting with SuccessablesYap.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 TTACTAA, 0.
  2. positive strand, negative direction, looking for TTACTAA, 1, TTACTAA at 3472.
  3. positive strand, positive direction, looking for TTACTAA, 0.
  4. negative strand, positive direction, looking for TTACTAA, 0.
  5. inverse complement, negative strand, negative direction, looking for TTAGTAA, 0.
  6. inverse complement, positive strand, negative direction, looking for TTAGTAA, 0.
  7. inverse complement, positive strand, positive direction, looking for TTAGTAA, 0.
  8. inverse complement, negative strand, positive direction, looking for TTAGTAA, 0.

Yap (4560-2846) UTRs

  1. Positive strand, negative direction: TTACTAA at 3472.

Yap random dataset samplings

  1. Yapr0: 0.
  2. Yapr1: 1, TTACTAA at 4451.
  3. Yapr2: 1, TTACTAA at 2374.
  4. Yapr3: 0.
  5. Yapr4: 1, TTACTAA at 3669.
  6. Yapr5: 0.
  7. Yapr6: 1, TTACTAA at 1423.
  8. Yapr7: 0.
  9. Yapr8: 0.
  10. Yapr9: 0.
  11. Yapr0ci: 0.
  12. Yapr1ci: 1, TTAGTAA at 1724.
  13. Yapr2ci: 0.
  14. Yapr3ci: 1, TTAGTAA at 916.
  15. Yapr4ci: 1, TTAGTAA at 2301.
  16. Yapr5ci: 0.
  17. Yapr6ci: 0.
  18. Yapr7ci: 0.
  19. Yapr8ci: 0.
  20. Yapr9ci: 1, TTAGTAA at 4015.

Yapr arbitrary (evens) (4560-2846) UTRs

  1. Yapr4: TTACTAA at 3669.

Yapr alternate (odds) (4560-2846) UTRs

  1. Yapr1: TTACTAA at 4451.
  2. Yapr9ci: TTAGTAA at 4015.

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

  1. Yapr2: TTACTAA at 2374.
  2. Yapr6: TTACTAA at 1423.
  3. Yapr4ci: TTAGTAA at 2301.

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

  1. Yapr1ci: TTAGTAA at 1724.
  2. Yapr3ci: TTAGTAA at 916.
  3. Yapr9ci: TTAGTAA at 4015.

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

  1. Yapr1ci: TTAGTAA at 1724.
  2. Yapr3ci: TTAGTAA at 916.
  3. Yapr9ci: TTAGTAA at 4015.

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

  1. Yapr2: TTACTAA at 2374.
  2. Yapr4: TTACTAA at 3669.
  3. Yapr6: TTACTAA at 1423.
  4. Yapr4ci: TTAGTAA at 2301.

Yap analysis and results

Main article: Complex locus A1BG and ZNF497 § Yaps

At "least four Yap proteins bind most efficiently to TTACTAA, a sequence that differs at position ±2 from the optimal AP-1 site (TGACTCA)".[2][1]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 1 2 0.5 0.5
Randoms UTR arbitrary negative 1 10 0.1 0.15
Randoms UTR alternate negative 2 10 0.2 0.15
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 0 2 0 0
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 0 10 0 0
Randoms Proximal alternate positive 0 10 0 0
Reals Distal negative 0 2 0 0
Randoms Distal arbitrary negative 3 10 0.3 0.3
Randoms Distal alternate negative 3 10 0.3 0.3
Reals Distal positive 0 2 0 0
Randoms Distal arbitrary positive 3 10 0.3 0.35
Randoms Distal alternate positive 4 10 0.4 0.35

Comparison:

The occurrences of real Yap UTRs are greater than the randoms. This suggests that the real Yaps are likely active or activable.

Yap response element samplings

Copying a responsive elements consensus sequence T(G/T)ACT(A/C)A and putting the sequence in "⌘F" finds none between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence T(G/T)ACT(A/C)A (starting with SuccessablesYapR.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: 0.
  2. Positive strand, negative direction: 1, TTACTAA at 3472.
  3. Negative strand, positive direction: 0.
  4. Positive strand, positive direction: 2, TTACTCA at 3447, TGACTAA at 2676.
  5. inverse complement, negative strand, negative direction: 0.
  6. inverse complement, positive strand, negative direction: 0.
  7. inverse complement, negative strand, positive direction: 0.
  8. inverse complement, positive strand, positive direction: 0.

YapR (4560-2846) UTRs

  1. Positive strand, negative direction: TTACTAA at 3472.

YapR positive direction (4050-1) distal promoters

  1. Positive strand, positive direction: TTACTCA at 3447, TGACTAA at 2676.

YapR random dataset samplings

  1. YapRr0: 0.
  2. YapRr1: 1, TTACTAA at 4451.
  3. YapRr2: 2, TTACTCA at 4306, TTACTAA at 2374.
  4. YapRr3: 0.
  5. YapRr4: 4, TTACTAA at 3669, TGACTCA at 2963, TTACTCA at 2650, TTACTCA at 1137.
  6. YapRr5: 0.
  7. YapRr6: 2, TGACTCA at 2045, TTACTAA at 1423.
  8. YapRr7: 1, TGACTAA at 4046.
  9. YapRr8: 1, TTACTCA at 2158.
  10. YapRr9: 3, TGACTAA at 4474, TGACTAA at 3706, TGACTCA at 2082.
  11. YapRr0ci: 1, TTAGTCA at 3188.
  12. YapRr1ci: 1, TTAGTAA at 1724.
  13. YapRr2ci: 2, TGAGTAA at 3017, TTAGTCA at 2899.
  14. YapRr3ci: 1, TTAGTAA at 916.
  15. YapRr4ci: 3, TGAGTAA at 3403, TTAGTAA at 2301, TGAGTCA at 2248.
  16. YapRr5ci: 2, TGAGTCA at 4249, TTAGTCA at 1354.
  17. YapRr6ci: 0.
  18. YapRr7ci: 0.
  19. YapRr8ci: 1, TGAGTAA at 1966.
  20. YapRr9ci: 1, TTAGTAA at 4015.

YapRr arbitrary (evens) (4560-2846) UTRs

  1. YapRr2: TTACTCA at 4306.
  2. YapRr4: TTACTAA at 3669, TGACTCA at 2963.
  3. YapRr0ci: TTAGTCA at 3188.
  4. YapRr2ci: TGAGTAA at 3017, TTAGTCA at 2899.
  5. YapRr4ci: TGAGTAA at 3403.

YapRr alternate (odds) (4560-2846) UTRs

  1. YapRr1: TTACTAA at 4451.
  2. YapRr7: TGACTAA at 4046.
  3. YapRr9: TGACTAA at 4474, TGACTAA at 3706.
  4. YapRr5ci: TGAGTCA at 4249.
  5. YapRr9ci: TTAGTAA at 4015.

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

  1. YapRr2: TTACTCA at 4306.

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

  1. YapRr4: TTACTCA at 2650.

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

  1. YapRr5ci: TGAGTCA at 4249.

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

  1. YapRr4: TTACTCA at 1137.
  2. YapRr6: TGACTCA at 2045, TTACTAA at 1423.
  3. YapRr8: TTACTCA at 2158.
  4. YapRr4ci: TTAGTAA at 2301, TGAGTCA at 2248.
  5. YapRr8ci: TGAGTAA at 1966.

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

  1. YapRr9: TGACTCA at 2082.
  2. YapRr1ci: TTAGTAA at 1724.
  3. YapRr3ci: TTAGTAA at 916.
  4. YapRr5ci: TTAGTCA at 1354.

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

  1. YapRr7: TGACTAA at 4046.
  2. YapRr9: TGACTAA at 3706, TGACTCA at 2082.
  3. YapRr1ci: TTAGTAA at 1724.
  4. YapRr3ci: TTAGTAA at 916.
  5. YapRr5ci: TTAGTCA at 1354.
  6. YapRr9ci: TTAGTAA at 4015.

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

  1. YapRr2: TTACTAA at 2374.
  2. YapRr4: TTACTAA at 3669, TGACTCA at 2963, TTACTCA at 2650, TTACTCA at 1137.
  3. YapRr6: TGACTCA at 2045, TTACTAA at 1423.
  4. YapRr8: TTACTCA at 2158.
  5. YapRr0ci: TTAGTCA at 3188.
  6. YapRr2ci: TGAGTAA at 3017, TTAGTCA at 2899.
  7. YapRr4ci: TGAGTAA at 3403, TTAGTAA at 2301, TGAGTCA at 2248.
  8. YapRr8ci: TGAGTAA at 1966.

YapR analysis and results

Main article: Complex locus A1BG and ZNF497 § YapRs

"Yap1p recognizes YRE (Yap1p response elements, 5'-TKACTMA-3') in the promoters of genes involved in redox homeostasis and in xenobiotic export at the plasma membrane."[3]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 1 2 0.5 0.5 ± 0.5 (--0,+-1)
Randoms UTR arbitrary negative 7 10 0.7 0.65
Randoms UTR alternate negative 6 10 0.6 0.65
Reals Core negative 0 2 0 0
Randoms Core arbitrary negative 1 10 0 0
Randoms Core alternate negative 0 10 0 0
Reals Core positive 0 2 0 0
Randoms Core arbitrary positive 1 10 0.1 0.05
Randoms Core alternate positive 0 10 0 0.05
Reals Proximal negative 0 2 0 0
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 0.05
Randoms Proximal alternate positive 0 10 0 0.05
Reals Distal negative 0 2 0 0
Randoms Distal arbitrary negative 7 10 0.7 0.55
Randoms Distal alternate negative 4 10 0.4 0.55
Reals Distal positive 2 2 1 1 ± 1 (-+0,++2)
Randoms Distal arbitrary positive 7 10 0.7 1.1 ± 0.04
Randoms Distal alternate positive 15 10 1.5 1.1 ± 0.04

Comparison:

The occurrences of real YapR UTRs and distals are greater than the randoms. This suggests that the real YapRs are likely active or activable.

Acknowledgements

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

See also

References

  1. ↑ 1.0 1.1 1.2 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.
  2. ↑ 2.0 2.1 Lisete Fernandes, Claudina Rodrigues-Pousada, Kevin Struhl (December 1997). "Yap, a novel family of eight bZIP proteins in Saccharomyces cerevisiae with distinct biological functions". Molecular and Cellular Biology. 17 (12): 6982–6993. doi:10.1128/MCB.17.12.6982. Retrieved 11 March 2021.
  3. ↑ Hélène Salin, Vivienne Fardeau, Eugenia Piccini, Gaelle Lelandais, Véronique Tanty, Sophie Lemoine, Claude Jacq, and Frédéric Devaux (15 July 2008). "Structure and properties of transcriptional networks driving selenite stress response in yeasts". BMC Genomics. 9: 933. doi:10.1186/1471-2164-9-333. PMID 18627600. Retrieved 27 February 2021.

External links


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