Hac1p gene transcriptions

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

"The [unfolded protein response] UPR has been shown to play important roles in overexpression and secretion of some recombinant proteins [9]. Manipulating the level of transcription factors and [endoplasmic reticulum] ER chaperones in the UPR pathway improved secretion of recombinant proteins [10, 11]. An important characteristic of the UPR is that it is directly linked to transcription activation processes governed by ER stress conditions. In Sachcharomyces cerevisiae this process is mediated by a unique mechanism involving cooperative action of Hac1 transcription factor (TF) and a short conserved DNA sequence referred to as unfolded protein response element (UPRE) in the promoter of UPR target genes [12]. The UPRE regulatory cis acting element lies within 22-bp upstream of the promoter of UPR responsive genes, which is crucial for transcriptional induction under ER stress [13]. The best characterized UPRE core sequence was UPRE-1 (CANCNTG) from S. cerevisiae (for examples from KAR2, CAGCGTG and PDI1, CACCGTG) [13, 14]. The similar UPRE-1 is also found in the promoter region of the P. pastoris KAR2 (CAGCGTG), INO1 (CAACTTG) and HAC1 (CAACTTG) genes [15]. The presence of an HAC1 UPRE implies that Hac1p can up-regulate its own transcription. Unconventional splicing of HAC1 mRNA after ER stress signaling generates the active form of basic leucine zipper (bZIP) transcription factor Hac1p, which binds to the UPRE [16]."[1]

Human genes

Interactions

Consensus sequences

The upstream activating sequence (UAS) for Hac1p is 5'-CAGCGTG-3'.[2]

KAR2 samplings

Main article: Model samplings

Copying 5'-CAGCGTG-3' 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 CAGCGTG (starting with SuccessablesHac.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 CAGCGTG, 0.
  2. negative strand, positive direction, looking for CAGCGTG, 0.
  3. positive strand, negative direction, looking for CAGCGTG, 1, CAGCGTG at 740.
  4. positive strand, positive direction, looking for CAGCGTG, 0.
  5. complement, negative strand, negative direction, looking for GTCGCAC, 1, GTCGCAC at 740.
  6. complement, negative strand, positive direction, looking for GTCGCAC, 0.
  7. complement, positive strand, negative direction, looking for GTCGCAC, 0.
  8. complement, positive strand, positive direction, looking for GTCGCAC, 0.
  9. inverse complement, negative strand, negative direction, looking for CACGCTG, 0.
  10. inverse complement, negative strand, positive direction, looking for CACGCTG, 1, CACGCTG at 778.
  11. inverse complement, positive strand, negative direction, looking for CACGCTG, 0.
  12. inverse complement, positive strand, positive direction, looking for CACGCTG, 0.
  13. inverse negative strand, negative direction, looking for GTGCGAC, 0.
  14. inverse negative strand, positive direction, looking for GTGCGAC, 0.
  15. inverse positive strand, negative direction, looking for GTGCGAC, 0.
  16. inverse positive strand, positive direction, looking for GTGCGAC, 1, GTGCGAC at 778.

KAR2 distal promoters

Main article: Distal promoter gene transcriptions
  1. Positive strand, negative direction: CAGCGTG at 740.


  1. Negative strand, positive direction: CACGCTG at 778.

KAR2 random dataset samplings

  1. KAR2r0: 1, CAGCGTG at 3076.
  2. KAR2r1: 0.
  3. KAR2r2: 0.
  4. KAR2r3: 0.
  5. KAR2r4: 1, CAGCGTG at 1562.
  6. KAR2r5: 1, CAGCGTG at 370.
  7. KAR2r6: 0.
  8. KAR2r7: 0.
  9. KAR2r8: 0.
  10. KAR2r9: 0.
  11. KAR2r0ci: 0.
  12. KAR2r1ci: 0.
  13. KAR2r2ci: 0.
  14. KAR2r3ci: 0.
  15. KAR2r4ci: 0.
  16. KAR2r5ci: 0.
  17. KAR2r6ci: 0.
  18. KAR2r7ci: 0.
  19. KAR2r8ci: 0.
  20. KAR2r9ci: 0.

KAR2r UTRs

  1. KAR2r0: CAGCGTG at 3076.

KAR2r distal promoters

  1. KAR2r4: CAGCGTG at 1562.


  1. KAR2r5: CAGCGTG at 370.

Hac1 analysis and results

Main article: Complex locus A1BG and ZNF497 § KAR2s

The upstream activating sequence (UAS) for Hac1p is CAGCGTG.[2]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 0 2 0 0
Randoms UTR arbitrary negative 1 10 0.1 0.05
Randoms UTR alternate negative 0 10 0 0.05
Reals Core negative 0 2 0 0
Randoms Core negative 0 10 0 0
Reals Core positive 0 2 0 0
Randoms Core positive 0 10 0 0
Reals Proximal negative 0 2 0 0
Randoms Proximal negative 0 10 0 0
Reals Proximal positive 0 2 0 0
Randoms Proximal positive 0 10 0 0
Reals Distal negative 1 2 0.5 0.5
Randoms Distal negative 1 10 0.1 0.1
Reals Distal positive 1 2 0.5 0.5
Randoms Distal positive 1 10 0.1 0.1

Comparison:

The occurrences of real unfolded protein response elements are larger than the randoms. This suggests that the real unfolded protein response elements are likely active or activable.

UPRE-1 samplings

For the Basic programs testing consensus sequence CANCNTG (starting with SuccessablesUPRE.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 CANCNTG, 3, CACCGTG at 2664, CATCATG at 2342, CATCTTG at 286, and complements.
  2. negative strand, positive direction, looking for CANCNTG, 7, CATCATG at 4364, CATCCTG at 4185, CACCATG at 3827, CACCCTG at 2967, CACCATG at 2473, CAACCTG at 946, CAACCTG at 846.
  3. positive strand, negative direction, looking for CANCNTG, 21, CAGCCTG at 4348, CAGCCTG at 4036, CATCCTG at 3905, CACCCTG at 3743, CAGCCTG at 3297, CAGCCTG at 3127, CAGCCTG at 2769, CAACATG at 2613, CAGCCTG at 2434, CAGCATG at 2276, CAGCCTG at 2267, CAACATG at 2151, CAGCCTG at 2008, CATCCTG at 1840, CAACATG at 1206, CAGCCTG at 1197, CAGCCTG at 898, CAGCGTG at 740, CAGCCTG at 731, CATCCTG at 595, CAGCCTG at 507.
  4. positive strand, positive direction, looking for CANCNTG, 0.
  5. complement, negative strand, negative direction, looking for GTNGNAC, 21, GTCGGAC at 4348, GTCGGAC at 4036, GTAGGAC at 3905, GTGGGAC at 3743, GTCGGAC at 3297, GTCGGAC at 3127, GTCGGAC at 2769, GTTGTAC at 2613, GTCGGAC at 2434, GTCGTAC at 2276, GTCGGAC at 2267, GTTGTAC at 2151, GTCGGAC at 2008, GTAGGAC at 1840, GTTGTAC at 1206, GTCGGAC at 1197, GTCGGAC at 898, GTCGCAC at 740, GTCGGAC at 731, GTAGGAC at 595, GTCGGAC at 507.
  6. complement, negative strand, positive direction, looking for GTNGNAC, 7, GTAGTAC at 4364, GTAGGAC at 4185, GTGGTAC at 3827, GTGGGAC at 2967, GTGGTAC at 2473, GTTGGAC at 946, GTTGGAC at 846.
  7. complement, positive strand, negative direction, looking for GTNGNAC, 3, GTGGCAC at 2664, GTAGTAC at 2342, GTAGAAC at 286.
  8. complement, positive strand, positive direction, looking for GTNGNAC, 0.
  9. inverse complement, negative strand, negative direction, looking for CANGNTG, 0.
  10. inverse complement, negative strand, positive direction, looking for CANGNTG, 7, CAGGCTG at 3639, CAGGATG at 3574, CAGGGTG at 3539, CATGTTG at 2476, CAGGCTG at 2319, CATGATG at 2143, CACGCTG at 778.
  11. inverse complement, positive strand, negative direction, looking for CANGNTG, 10, CATGGTG at 4109, CAAGGTG at 3143, CATGGTG at 2616, CACGGTG at 2526, CATGCTG at 2325, CATGGTG at 2279, CATGTTG at 1852, CAGGCTG at 1463, CATGGTG at 1209, CACGGTG at 655.
  12. inverse complement, positive strand, positive direction, looking for CANGNTG, 2, CACGTTG at 2802, CATGGTG at 2599.
  13. inverse negative strand, negative direction, looking for GTNCNAC, 10, GTACCAC at 4109, GTTCCAC at 3143, GTACCAC at 2616, GTGCCAC at 2526, GTACGAC at 2325, GTACCAC at 2279, GTACAAC at 1852, GTCCGAC at 1463, GTACCAC at 1209, GTGCCAC at 655.
  14. inverse negative strand, positive direction, looking for GTNCNAC, 2, GTGCAAC at 2802, GTACCAC at 2599.
  15. inverse positive strand, negative direction, looking for GTNCNAC, 0.
  16. inverse positive strand, positive direction, looking for GTNCNAC, 7, GTCCGAC at 3639, GTCCTAC at 3574, GTCCCAC at 3539, GTACAAC at 2476, GTCCGAC at 2319, GTACTAC at 2143, GTGCGAC at 778.

UPRE-1 random dataset samplings

  1. RDr0: 0.
  2. RDr1: 0.
  3. RDr2: 0.
  4. RDr3: 0.
  5. RDr4: 0.
  6. RDr5: 0.
  7. RDr6: 0.
  8. RDr7: 0.
  9. RDr8: 0.
  10. RDr9: 0.
  11. RDr0ci: 0.
  12. RDr1ci: 0.
  13. RDr2ci: 0.
  14. RDr3ci: 0.
  15. RDr4ci: 0.
  16. RDr5ci: 0.
  17. RDr6ci: 0.
  18. RDr7ci: 0.
  19. RDr8ci: 0.
  20. RDr9ci: 0.

RDr UTRs

RDr core promoters

RDr proximal promoters

RDr distal promoters

UPRE-1 analysis and results

Main article: Complex locus A1BG and ZNF497 § UPRE-1s

"The best characterized UPRE core sequence was UPRE-1 (CANCNTG) from S. cerevisiae".[1]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 0 2 0 0
Randoms UTR arbitrary negative 0 10 0 0
Randoms UTR alternate negative 0 10 0 0
Reals Core negative 0 2 0 0
Randoms Core negative 0 10 0 0
Reals Core positive 0 2 0 0
Randoms Core positive 0 10 0 0
Reals Proximal negative 0 2 0 0
Randoms Proximal negative 0 10 0 0
Reals Proximal positive 0 2 0 0
Randoms Proximal positive 0 10 0 0
Reals Distal negative 0 2 0 0
Randoms Distal negative 0 10 0 0
Reals Distal positive 0 2 0 0
Randoms Distal positive 0 10 0 0

Comparison:

The occurrences of real responsive element consensus sequences are larger than the randoms. This suggests that the real responsive element consensus sequences are likely active or activable.

See also

References

  1. ↑ 1.0 1.1 Niwed Kullawong, Sutipa Tanapongpipat, Lily Eurwilaichitr and Witoon Tirasophon (2018). "Unfolded Protein Response (UPR) Induced Hybrid Promoters for Heterologous Gene Expression in Pichia pastoris" (PDF). Chiang Mai Journal of Science. 45 (7): 2554–2565. Retrieved 11 January 2021.
  2. ↑ 2.0 2.1 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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