Hac1p gene transcriptions: Difference between revisions

Revision as of 12:55, 12 January 2021

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

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:

negative strand, negative direction, looking for CAGCGTG, 0.
negative strand, positive direction, looking for CAGCGTG, 0.
positive strand, negative direction, looking for CAGCGTG, 1, CAGCGTG at 740.
positive strand, positive direction, looking for CAGCGTG, 0.
complement, negative strand, negative direction, looking for GTCGCAC, 1, GTCGCAC at 740.
complement, negative strand, positive direction, looking for GTCGCAC, 0.
complement, positive strand, negative direction, looking for GTCGCAC, 0.
complement, positive strand, positive direction, looking for GTCGCAC, 0.
inverse complement, negative strand, negative direction, looking for CACGCTG, 0.
inverse complement, negative strand, positive direction, looking for CACGCTG, 1, CACGCTG at 778.
inverse complement, positive strand, negative direction, looking for CACGCTG, 0.
inverse complement, positive strand, positive direction, looking for CACGCTG, 0.
inverse negative strand, negative direction, looking for GTGCGAC, 0.
inverse negative strand, positive direction, looking for GTGCGAC, 0.
inverse positive strand, negative direction, looking for GTGCGAC, 0.
inverse positive strand, positive direction, looking for GTGCGAC, 1, GTGCGAC at 778.

KAR2 distal promoters

Positive strand: CAGCGTG at 740, and complement.

Negative strand: CACGCTG at 778, and complement.

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:

negative strand, negative direction, looking for CANCNTG, 3, CACCGTG at 2664, CATCATG at 2342, CATCTTG at 286, and complements.
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.
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.
positive strand, positive direction, looking for CANCNTG, 0.
complement, negative strand, negative direction, looking for GTNGNAC, 0.
complement, negative strand, positive direction, looking for GTNGNAC, 0.
complement, positive strand, negative direction, looking for GTNGNAC, 0.
complement, positive strand, positive direction, looking for GTNGNAC, 0.
inverse complement, negative strand, negative direction, looking for CANGNTG, 0.
inverse complement, negative strand, positive direction, looking for CANGNTG, 0.
inverse complement, positive strand, negative direction, looking for CANGNTG, 0.
inverse complement, positive strand, positive direction, looking for CANGNTG, 0.
inverse negative strand, negative direction, looking for AAAAAAAA, 0.
inverse negative strand, positive direction, looking for AAAAAAAA, 0.
inverse positive strand, negative direction, looking for AAAAAAAA, 0.
inverse positive strand, positive direction, looking for AAAAAAAA, 0.

References

↑ 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.
↑ 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

[Kullawong-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.

[Tang-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.

[1]

[2]

@@ Line 69: / Line 69: @@
 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:
 # negative strand, negative direction, looking for CANCNTG, 3, CACCGTG at 2664, CATCATG at 2342, CATCTTG at 286, and complements.
-# negative strand, positive direction, looking for CANCNTG, 0.
+# 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.
-# positive strand, negative direction, looking for CANCNTG, 0.
+# 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.
 # positive strand, positive direction, looking for CANCNTG, 0.
-# complement, negative strand, negative direction, looking for TTTTTTTT, 0.
+# complement, negative strand, negative direction, looking for GTNGNAC, 0.
-# complement, negative strand, positive direction, looking for TTTTTTTT, 0.
+# complement, negative strand, positive direction, looking for GTNGNAC, 0.
-# complement, positive strand, negative direction, looking for TTTTTTTT, 0.
+# complement, positive strand, negative direction, looking for GTNGNAC, 0.
-# complement, positive strand, positive direction, looking for TTTTTTTT, 0.
+# complement, positive strand, positive direction, looking for GTNGNAC, 0.
-# inverse complement, negative strand, negative direction, looking for TTTTTTTT, 0.
+# inverse complement, negative strand, negative direction, looking for CANGNTG, 0.
-# inverse complement, negative strand, positive direction, looking for TTTTTTTT, 0.
+# inverse complement, negative strand, positive direction, looking for CANGNTG, 0.
-# inverse complement, positive strand, negative direction, looking for TTTTTTTT, 0.
+# inverse complement, positive strand, negative direction, looking for CANGNTG, 0.
-# inverse complement, positive strand, positive direction, looking for TTTTTTTT, 0.
+# inverse complement, positive strand, positive direction, looking for CANGNTG, 0.
 # inverse negative strand, negative direction, looking for AAAAAAAA, 0.
 # inverse negative strand, positive direction, looking for AAAAAAAA, 0.

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recognition element gene transcriptions DREB box gene transcriptions E2 box gene transcriptions EIF4E basal element gene transcriptions EIN3 binding site gene transcriptions Enhancer activity copy gene transcriptions E box gene transcriptions Element gene transcriptions Endoplasmic reticulum stress response element gene transcriptions Endosperm expression gene transcriptions Enhancer box gene transcriptions Estrogen response element gene transcriptions Ethylene responsive element gene transcriptions Families of TATA box genes F box gene transcriptions Focused promoter gene transcriptions Forkhead box gene transcriptions Fur box gene transcriptions GAAC element gene transcriptions Gal4p gene transcriptions Γ-interferon activated sequence gene transcriptions GARE gene transcriptions GA responsive complex gene transcriptions GATA gene transcriptions G box gene transcriptions GC box gene transcriptions GCC box gene transcriptions Gcn4p gene transcriptions Gcr1p gene transcriptions Gene expressions General factor II D gene transcriptions General regulatory factors General transcription factor II A gene transcriptions General transcription factor II B gene transcriptions General transcription factor II D gene transcriptions General transcription factor II F gene transcriptions General transcription factor II H gene transcriptions General transcription factor gene transcriptions Gene transcriptions GGC triplet gene transcriptions Gibberellin responsive element gene transcriptions GLM box gene transcriptions Glucocorticoid response element gene transcriptions Grainy head gene transcriptions Grainy head transcription factor gene transcriptions Growth hormone response element gene transcriptions GT boxes Hac1p gene transcriptions Hair color gene expressions H and ACA box gene transcriptions H box gene transcriptions Heat-responsive element gene transcriptions Heat shock elements Hex sequence gene transcriptions HMG box gene transcriptions HNF gene transcriptions Homeobox gene transcriptions Hsf1p gene transcriptions HY box gene transcriptions Hybrid C, A boxes Hybrid C, G boxes Hybrid C, T boxes Hypoxia-inducible factor gene transcriptions Hypoxia response elements I box gene transcriptions Immunoglobulin like domain containing family Initiator element gene transcriptions Initiator-like element gene transcriptions Inositol/choline-responsive elements Interaction gene transcriptions Interferon regulatory factors Inverse copy gene transcriptions Jasmonic acid-responsive element gene transcriptions K-boxes Kozak sequence gene transcriptions Kruppel-associated box gene transcriptions Krüppel-like factor gene transcriptions L box gene transcriptions Leu3 gene transcriptions M35 box gene transcriptions MADS box gene transcriptions Maf recognition element gene transcriptions M box gene transcriptions Mcm1 regulatory factor gene transcriptions Met3 gene transcriptions Met31p box gene transcriptions Metal responsive element gene transcriptions Middle sporulation element gene transcriptions Mig1p gene transcriptions Model samplings Motif ten element gene transcriptions Msn2,4p gene transcriptions Musashi binding element gene transcriptions MYB recognition element gene transcriptions Myelocytomatosis transcription factor gene transcriptions Myocyte enhancer factor gene transcriptions N-boxes Nanos/Pumilio response element Ndt80p gene transcriptions Nuclear factor 1 Nuclear factor 𝜿B Nuclear factor gene transcriptions Nuclear factor of activated T cell gene transcriptions (NFAT) Nuclear factor Y gene transcriptions Nutrient-sensing response element gene transcriptions Oaf1p gene transcriptions ORE1 binding site gene transcriptions p53 response element gene transcriptions P63 DNA-binding site gene transcriptions P box gene transcriptions Pdr1,3p gene transcriptions Peroxisome proliferator hormone response element gene transcriptions Phosphate starvation-response transcription factor gene transcriptions Pollen1 element gene transcriptions Polycomb response element gene transcriptions Preinitiation complex Preinitiation complex gene transcriptions Pribnow box gene transcriptions Prolamin box gene transcriptions Promoter gene transcriptions Proximal promoter gene transcriptions Promoter occurrence gene transcriptions Pyrimidine box gene transcriptions Q element gene transcriptions Rap1 regulatory factor gene transcriptions Reb1 general regulatory factor gene transcriptions Retinoblastoma control element gene transcriptions Retinoic acid response element gene transcriptions Rgt1p gene transcriptions Rlm1p gene transcriptions RNA polymerase II gene transcriptions RNA polymerase II holoenzyme complex Root specific element gene transcriptions ROR-response element gene transcriptions Rox1p gene transcriptions Rpn4p gene transcriptions R response element gene transcriptions SARE gene transcriptions Seed-specific element gene transcriptions Serum response element gene transcriptions Servenius sequence gene transcriptions Shoot specific element gene transcriptions Sip4p gene transcriptions Smp1p gene transcriptions Sp1 gene transcriptions Spaceflight gene expressions Specificity protein gene transcriptions STAT gene transcriptions Ste12p gene transcriptions Sterol response element gene transcriptions Sucrose box gene transcriptions Synaptic Activity-Responsive Elements TACTAAC box gene transcriptions TAGteam gene transcriptions Tapetum box gene transcriptions TATA binding protein associated factor gene transcriptions TATA binding protein gene transcriptions TATA box actin/cytoskeleton/contractile family TATA box albumin family TATA box aldolase family TATA box alkaline phosphatase family TATA box annexin family TATA box cytochrome superfamily TATA box gene transcriptions TATA box heat shock family TATA box histone family TATA box human genes TATA box keratin family TATA box lipase family TATA box peptidase family TATA box platelet-derived growth factor family TATA box selenium-binding family TATA box serine protease family TATA box serpin superfamily TATA box transforming growth factor superfamily TATA box trefoil family TATA box tumor necrosis factor superfamily TATA box zinc metalloenzyme family TAT box gene transcriptions TATC box gene transcriptions Tbf1 regulatory factor gene transcriptions T box gene transcriptions TCCACCATA element gene transcriptions TC element gene transcriptions TCT gene transcriptions TEA consensus sequence gene transcriptions Tec1p gene transcriptions Telomeric repeat DNA-binding factor gene transcriptions Tetradecanoylphorbol-13-acetate response element gene transcriptions TGF-β control elements (TCEs) TGF-β inhibitory elements (TIEs) Thyroid hormone response element gene transcriptions Transcriptional regulation Transcription bubble gene transcriptions Transcription factor gene transcriptions Transcription factor 3 gene transcriptions Transcription factory gene transcriptions Transcription start site gene transcriptions Translational control sequence gene transcriptions Tryptophan residue U box gene transcriptions Unfolded protein response element gene transcriptions Upstream response element gene transcriptions Upstream stimulatory factor gene transcriptions UTR promoter gene transcriptions V and P box gene transcriptions V box gene transcriptions Vhr1p gene transcriptions Vitamin D response element gene transcriptions W box gene transcriptions X box gene transcriptions Xbp1p gene transcriptions X core promoter element gene transcriptions Xenobiotic response element gene transcriptions Xenobiotic responsive element gene transcriptions Yap1p,2p gene transcriptions Y box gene transcriptions YY1 gene transcriptions Zap1p gene transcriptions Z box gene transcriptions Zinc responsive element gene transcriptions