Copper response element gene transcriptions

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

"Chlamydomonas reinhardtii activates the transcription of the Cyc6 and the Cpx1 genes (encoding cytochrome c₆ and coprogen oxidase) in response to copper deficiency."^[1]

Human genes

Gene expressions

"Mac1p-dependent adaptation to copper deficiency involves the coordinate expression of genes, CTR1, CTR3, FRE1, and FRE7, encoding assimilatory components, through copper-response elements associated with each of these genes (10., 11., 12.)."^[1]

The "Cyc6 gene contains at least two copper-response elements (CuREs) (28)."^[1]

Interactions

Consensus sequences

"A consensus copper-response element [CuRE] TTTGC(T/G)C(A/G) (12) is a binding site for Mac1p."^[1]

"An additional EMSA result demonstrated that [Aspergillus fumigatus (Af)] AfMac1 directly binds to a copper response element in the promoter regions of the ctrA2 and ctrC genes with a defined consensus DNA motif (5′-TGTGCTCA-3′) (Park et al., 2017^[2]), which is strikingly similar to the Mac1-binding motif in S. cerevisiae (Jamison McDaniels et al., 1999; Keller et al., 2000), suggesting that the mechanism of Mac1-mediated copper homeostasis may be conserved across fungal species."^[3]

Binding site for

Hypotheses

A1BG has no regulatory elements in either promoter.
A1BG is not transcribed by a regulatory element.
No regulatory element participates in the transcription of A1BG.

CuRE (Quinn) samplings

Copying a responsive elements consensus sequence TTTGC(G/T)C(A/G) 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 TTTGC(G/T)C(A/G) (starting with SuccessablesCuRE.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 TTTGC(G/T)C(A/G), 0.
positive strand, negative direction, looking for TTTGC(G/T)C(A/G), 0.
positive strand, positive direction, looking for TTTGC(G/T)C(A/G), 0.
negative strand, positive direction, looking for TTTGC(G/T)C(A/G), 0.
complement, negative strand, negative direction, looking for AAACG(A/C)G(C/T), 0.
complement, positive strand, negative direction, looking for AAACG(A/C)G(C/T), 0.
complement, positive strand, positive direction, looking for AAACG(A/C)G(C/T), 0.
complement, negative strand, positive direction, looking for AAACG(A/C)G(C/T), 0.
inverse complement, negative strand, negative direction, looking for (C/T)G(A/C)GCAAA, 0.
inverse complement, positive strand, negative direction, looking for (C/T)G(A/C)GCAAA, 1, CGCGCAAA at 163.
inverse complement, positive strand, positive direction, looking for (C/T)G(A/C)GCAAA, 0.
inverse complement, negative strand, positive direction, looking for (C/T)G(A/C)GCAAA, 0.
inverse negative strand, negative direction, looking for (A/G)C(G/T)CGTTT, 1, GCGCGTTT at 163.
inverse positive strand, negative direction, looking for (A/G)C(G/T)CGTTT, 0.
inverse positive strand, positive direction, looking for (A/G)C(G/T)CGTTT, 0.
inverse negative strand, positive direction, looking for (A/G)C(G/T)CGTTT, 0.

CuRE distal promoters

Positive strand, negative direction: CGCGCAAA at 163.

CuRE (Park) samplings

Copying a responsive elements consensus sequence TGTGCTCA 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 TGTGCTCA (starting with SuccessablesPark.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 TGTGCTCA, 0.
positive strand, negative direction, looking for TGTGCTCA, 0.
positive strand, positive direction, looking for TGTGCTCA, 0.
negative strand, positive direction, looking for TGTGCTCA, 0.
complement, negative strand, negative direction, looking for ACACGAGT, 0.
complement, positive strand, negative direction, looking for ACACGAGT, 0.
complement, positive strand, positive direction, looking for ACACGAGT, 0.
complement, negative strand, positive direction, looking for ACACGAGT, 0.
inverse complement, negative strand, negative direction, looking for TGAGCACA, 0.
inverse complement, positive strand, negative direction, looking for TGAGCACA, 0.
inverse complement, positive strand, positive direction, looking for TGAGCACA, 0.
inverse complement, negative strand, positive direction, looking for TGAGCACA, 1, TGAGCACA at 3740.
inverse negative strand, negative direction, looking for ACTCGTGT, 0.
inverse positive strand, negative direction, looking for ACTCGTGT, 0.
inverse positive strand, positive direction, looking for ACTCGTGT, 1, ACTCGTGT at 3740.
inverse negative strand, positive direction, looking for ACTCGTGT, 0.

CuRE (Park) distal promoters

Negative strand, positive direction: TGAGCACA at 3740.

Acknowledgements

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

References

↑ ^1.0 ^1.1 ^1.2 ^1.3 Jeanette M. Quinn, Paola Barraco, Mats Eriksson and Sabeeha Merchant (March 2000). "Coordinate Copper- and Oxygen-responsive Cyc6 and Cpx1 Expression in Chlamydomonas Is Mediated by the Same Element". Journal of Biological Chemistry. 275 (9): 6080–6089. doi:10.1074/jbc.275.9.6080. Retrieved 1 April 2021.
↑ Yong-Sung Park, Tae-Hyoung Kim and Cheol-Won Yun (3 July 2017). "Functional characterization of the copper transcription factor AfMac1 from Aspergillus fumigatus". Biochemical Journal. 474 (14): 2365–2378. doi:10.1042/BCJ20170191. Retrieved 2 April 2021.
↑ Jinxing Song, Rongpeng Li and Jihong Jiang (12 April 2019). "Copper Homeostasis in Aspergillus fumigatus: Opportunities for Therapeutic Development". Frontiers in Microbiology. 10: 774. doi:10.3389/fmicb.2019.00774. Retrieved 2 April 2021.

External links

[Quinn-1] 1.0 ^1.1 ^1.2 ^1.3 Jeanette M. Quinn, Paola Barraco, Mats Eriksson and Sabeeha Merchant (March 2000). "Coordinate Copper- and Oxygen-responsive Cyc6 and Cpx1 Expression in Chlamydomonas Is Mediated by the Same Element". Journal of Biological Chemistry. 275 (9): 6080–6089. doi:10.1074/jbc.275.9.6080. Retrieved 1 April 2021.

[Park-2] Yong-Sung Park, Tae-Hyoung Kim and Cheol-Won Yun (3 July 2017). "Functional characterization of the copper transcription factor AfMac1 from Aspergillus fumigatus". Biochemical Journal. 474 (14): 2365–2378. doi:10.1042/BCJ20170191. Retrieved 2 April 2021.

[Song-3] Jinxing Song, Rongpeng Li and Jihong Jiang (12 April 2019). "Copper Homeostasis in Aspergillus fumigatus: Opportunities for Therapeutic Development". Frontiers in Microbiology. 10: 774. doi:10.3389/fmicb.2019.00774. Retrieved 2 April 2021.

[1]

[2]

[3]

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