Ndt80p gene transcriptions

Jump to navigation Jump to search

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

"The Saccharomyces cerevisiae Ndt80 protein is the founding member of a class of p53-like transcription factors that is known as the NDT80/PhoG-like DNA-binding family."[1]

Ndt80 [Non-DiTyrosine 80] is a meiosis-specific transcription factor required for successful completion of meiosis and spore formation.[2] The DNA-binding domain of Ndt80 has been isolated, and the structure reveals that this protein is a member of the Ig-fold family of transcription factors.[3] Ndt80 also competes with the repressor SUM1 for binding to promoters containing MSEs.[4]

Direct "binding of Ndt80 to the [mid sporulation element CRCAAAA/T (Ozsarac et al. 1997)] MSE is necessary for activating transcription of the middle sporulation genes."[5]

"These genomic sequences were analysed for the presence of [...] middle sporulation elements (MSE) motif (5'-ACACAAA-3') using the NCBI BLAST tool."[6]

Human genes

Interactions

Consensus sequences

The upstream activating sequence (UAS) for the Ndt80p is 5'-DNCRCAAAW-3'.[7]

Ndt80 samplings

Copying DNCRCAAAW, (A/G/T)(A/C/G/T)C(A/G)CAAA(A/T), or TCCGCA 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 (A/G/T)(A/C/G/T)C(A/G)CAAA(A/T) (starting with SuccessablesNDT.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 (A/G/T)NC(A/G)CAAA(A/T), 0.
  2. positive strand, negative direction, looking for (A/G/T)NC(A/G)CAAA(A/T), 1, ACCACAAAA at 3767.
  3. positive strand, positive direction, looking for (A/G/T)NC(A/G)CAAA(A/T), 0.
  4. negative strand, positive direction, looking for (A/G/T)NC(A/G)CAAA(A/T), 0.
  5. complement, negative strand, negative direction, looking for (A/C/T)NG(C/T)GTTT(A/T), 1, TGGTGTTTT at 3767.
  6. complement, positive strand, negative direction, looking for (A/C/T)NG(C/T)GTTT(A/T), 0.
  7. complement, positive strand, positive direction, looking for (A/C/T)NG(C/T)GTTT(A/T), 0.
  8. complement, negative strand, positive direction, looking for (A/C/T)NG(C/T)GTTT(A/T), 0.
  9. inverse complement, negative strand, negative direction, looking for (A/T)TTTG(C/T)GN(A/C/T), 1, TTTTGTGTT at 3514.
  10. inverse complement, positive strand, negative direction, looking for (A/T)TTTG(C/T)GN(A/C/T), 0.
  11. inverse complement, positive strand, positive direction, looking for (A/T)TTTG(C/T)GN(A/C/T), 0.
  12. inverse complement, negative strand, positive direction, looking for (A/T)TTTG(C/T)GN(A/C/T), 0.
  13. inverse negative strand, negative direction, looking for (A/T)AAAC(A/G)CN(A/G/T), 0.
  14. inverse positive strand, negative direction, looking for (A/T)AAAC(A/G)CN(A/G/T), 1, AAAACACAA at 3514.
  15. inverse positive strand, positive direction, looking for (A/T)AAAC(A/G)CN(A/G/T), 0.
  16. inverse negative strand, positive direction, looking for (A/T)AAAC(A/G)CN(A/G/T), 0.

NDT (4560-2846) UTRs

  1. Negative strand, negative direction: TTTTGTGTT at 3514.
  2. Positive strand, negative direction: ACCACAAAA at 3767.

NDT random dataset samplings

  1. NDTr0: 2, ACCGCAAAT at 2807, TGCACAAAT at 1788.
  2. NDTr1: 3, TACGCAAAA at 4408, ATCACAAAA at 3175, ATCGCAAAA at 1775.
  3. NDTr2: 1, AGCACAAAA at 4322.
  4. NDTr3: 0.
  5. NDTr4: 1, GACACAAAA at 1971.
  6. NDTr5: 1, AGCGCAAAA at 752.
  7. NDTr6: 3, ACCACAAAT at 3077, GGCACAAAA at 970, TGCGCAAAT at 362.
  8. NDTr7: 2, TTCGCAAAT at 2393, GCCGCAAAT at 660.
  9. NDTr8: 2, GCCACAAAT at 3714, ACCGCAAAA at 2111.
  10. NDTr9: 1, GGCACAAAT at 4053.
  11. NDTr0ci: 0.
  12. NDTr1ci: 1, TTTTGTGGT at 284.
  13. NDTr2ci: 2, TTTTGTGGA at 4489, TTTTGCGGT at 39.
  14. NDTr3ci: 1, ATTTGCGCT at 3974.
  15. NDTr4ci: 1, TTTTGCGCT at 1428.
  16. NDTr5ci: 3, ATTTGTGGC at 3882, TTTTGTGTT at 324, TTTTGCGGT at 278.
  17. NDTr6ci: 1, TTTTGTGCA at 2655.
  18. NDTr7ci: 1, TTTTGTGGT at 495.
  19. NDTr8ci: 1, ATTTGCGGT at 2530.
  20. NDTr9ci: 1, TTTTGTGGT at 472.

NDTr arbitrary (evens) (4560-2846) UTRs

  1. NDTr2: AGCACAAAA at 4322.
  2. NDTr6: ACCACAAAT at 3077.
  3. NDTr8: GCCACAAAT at 3714.
  4. NDTr2ci: TTTTGTGGA at 4489.

NDTr alternate (odds) (4560-2846) UTRs

  1. NDTr1: TACGCAAAA at 4408, ATCACAAAA at 3175.
  2. NDTr9: GGCACAAAT at 4053.
  3. NDTr3ci: ATTTGCGCT at 3974.
  4. NDTr5ci: ATTTGTGGC at 3882.

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

  1. NDTr1: TACGCAAAA at 4408.

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

  1. NDTr2: AGCACAAAA at 4322.

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

  1. NDTr0: ACCGCAAAT at 2807.
  2. NDTr6ci: TTTTGTGCA at 2655.

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

  1. NDTr9: GGCACAAAT at 4053.

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

  1. NDTr0: TGCACAAAT at 1788.
  2. NDTr6: GGCACAAAA at 970, TGCGCAAAT at 362.
  3. NDTr8: ACCGCAAAA at 2111.
  4. NDTr2ci: TTTTGCGGT at 39.
  5. NDTr4ci: TTTTGCGCT at 1428.
  6. NDTr8ci: ATTTGCGGT at 2530.

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

  1. NDTr1: ATCGCAAAA at 1775.
  2. NDTr5: AGCGCAAAA at 752.
  3. NDTr7: TTCGCAAAT at 2393, GCCGCAAAT at 660.
  4. NDTr7ci: TTTTGTGGT at 495.
  5. NDTr9ci: TTTTGTGGT at 472.

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

  1. NDTr1: ATCACAAAA at 3175, ATCGCAAAA at 1775.
  2. NDTr5: AGCGCAAAA at 752.
  3. NDTr7: TTCGCAAAT at 2393, GCCGCAAAT at 660.
  4. NDTr3ci: ATTTGCGCT at 3974.
  5. NDTr7ci: TTTTGTGGT at 495.
  6. NDTr9ci: TTTTGTGGT at 472.

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

  1. NDTr0: ACCGCAAAT at 2807, TGCACAAAT at 1788.
  2. NDTr6: ACCACAAAT at 3077, GGCACAAAA at 970, TGCGCAAAT at 362.
  3. NDTr8: GCCACAAAT at 3714, ACCGCAAAA at 2111.
  4. NDTr2ci: TTTTGCGGT at 39.
  5. NDTr4ci: TTTTGCGCT at 1428.
  6. NDTr6ci: TTTTGTGCA at 2655.
  7. NDTr8ci: ATTTGCGGT at 2530.

NDT analysis and results

Main article: Complex locus A1BG and ZNF497 § NDTs

The upstream activating sequence (UAS) for the Ndt80p is DNCRCAAAW.[7]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 2 2 1 1 ± 0 (--1,+-1)
Randoms UTR arbitrary negative 4 10 0.4 0.45
Randoms UTR alternate negative 5 10 0.5 0.45
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 1 10 0.1 0.1
Randoms Core alternate positive 1 10 0.1 0.1
Reals Proximal negative 0 2 0 0
Randoms Proximal arbitrary negative 2 10 0.2 0.1
Randoms Proximal alternate negative 0 10 0 0.1
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 0.65
Randoms Distal alternate negative 6 10 0.6 0.65
Reals Distal positive 0 2 0 0
Randoms Distal arbitrary positive 8 10 0.8 0.95
Randoms Distal alternate positive 11 10 1.1 0.95

Comparison:

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

See also

References

  1. ↑ Margaret E Katz and Sarah Cooper (1 December 2015). "Extreme Diversity in the Regulation of Ndt80-Like Transcription Factors in Fungi". G3 Genes. 5 (12): 2783–2792. doi:10.1534/g3.115.021378. Retrieved 8 February 2021. Text "Genomes" ignored (help); Text "Genetics " ignored (help)
  2. ↑ Xu L, Ajimura M, Padmore R, Klein C, Kleckner N (December 1995). "NDT80, a meiosis-specific gene required for exit from pachytene in Saccharomyces cerevisiae". Molecular and Cellular Biology. 15 (12): 6572–81. doi:10.1128/MCB.15.12.6572. PMC 230910. PMID 8524222.
  3. ↑ Lamoureux JS, Stuart D, Tsang R, Wu C, Glover JN (November 2002). "Structure of the sporulation-specific transcription factor Ndt80 bound to DNA". The EMBO Journal. 21 (21): 5721–32. doi:10.1093/emboj/cdf572. PMC 131069. PMID 12411490.
  4. ↑ Hendrickson WA, Ward KB (October 1975). "Atomic models for the polypeptide backbones of myohemerythrin and hemerythrin". Biochemical and Biophysical Research Communications. 66 (4): 1349–56. doi:10.1016/0006-291x(75)90508-2. PMID 5.
  5. ↑ Shelley Chu and Ira Herskowitz (April 1, 1998). "Gametogenesis in Yeast Is Regulated by a Transcriptional Cascade Dependent on Ndt80". Molecular Cell. 1 (5): 685–96. doi:10.1016/S1097-2765(00)80068-4. PMID 9660952.
  6. ↑ J. Branco, M. Ola, R. M. Silva, E. Fonseca, N. C. Gomes, C. Martins-Cruz, A. P. Silva, A. Silva-Dias, C. Pina-Vaz, C. Erraught, L. Brennan, A. G. Rodrigues, G. Butler and I. M. Miranda (August 2017). "Impact of ERG3 mutations and expression of ergosterol genes controlled by UPC2 and NDT80 in Candida parapsilosis azole resistance". Clinical Microbiology and Infection. 23 (8): 575.e1–575.e8. doi:10.1016/j.cmi.2017.02.002. PMID 28196695. Retrieved 5 September 2020.
  7. ↑ 7.0 7.1 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

Retrieved from "https://www.wikidoc.org/index.php?title=Ndt80p_gene_transcriptions&oldid=1735981"