Cytokinin response regulator gene transcriptions

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

"Cytokinin fulfills its diverse roles in planta through a series of transcriptional responses."[1]

Human genes

Main article: Human genes

Gene expressions

Main article: Gene expressions

"In yeast two-hybrid analyses, the AHPs interact with various Arabidopsis histidine sensor kinases and Arabidopsis response regulators (ARRs) [20,24,25], consistent with their role in mediating phosphotransfer among these elements."[2]

"The 23 ARR genes fall into two main groups on the basis of their sequence similarities, domain structure and transcriptional response to cytokinin [27,28]. The type-A ARRs are comprised of a receiver domain and a short carboxyl terminus and their transcription is rapidly elevated in response to exogenous cytokinin; these are considered to be primary response genes [27,29,30]. The type-B ARRs, in addition to the receiver domain, have a carboxy-terminal output domain that has a DNA-binding GARP domain and a transcriptional activation domain. Transcription of the type-B ARRs is not altered by cytokinin."[2] Some of the ARRs are ARR1 - ARR20.[2][3]

Interactions

Main article: Interaction gene transcriptions

"Cytokinin employs a two-component multi-step phosphorelay for its perception and signaling transduction12–14. In Arabidopsis, there are three cytokinin receptors (ARABIDOPSIS HISTIDINE KINASEs; AHK2, 3, 4) and eleven type-B response regulators (ARABIDOSPIS RESPONSE REGULATORs; B-ARRs)8,15."[1]

"The cytokinin transcriptional response centrally affects the family of ARRs. Type-B ARRs (B-ARRs) are transcription factors (TFs) with a GARP-like DNA binding domain at their C-termini and a receiver domain at their N-termini. Type-A ARRs (A-ARRs) are similar to the N-termini receiver domain of B-ARRs but do not possess a DNA binding domain."[1]

Consensus sequences

Main article: Consensus sequence gene transcriptions

ARR1: AGATT(C/T), ARR10: (A/G)GATA(A/C)G, ARR12: (A/G)AGATA.[1]

"Type-B ARRs are transcription factors that localize to the nucleus [9,28,36]. A consensus DNA-binding sequence for type-B ARRs has been delineated (G/A)GGAT(T/C), and this sequence signature is found in the promoters of many of the cytokinin primary response genes [30]."[2]

"We used GeneSpring 5.0 software (Silicon Genetics, Redwood City, CA) to search for common motifs enriched within 1 kb upstream of the translational start site of the 17 genes that are consistently upregulated by cytokinin (those genes induced in six or more of the cytokinin treatments [...]). The sequence GATCTT was identified as a core sequence motif found significantly enriched in the upstream regions of this set of genes. [This] common upstream sequence motif GATCTT [occurs] on the forward strand, and [...] the complement of the motif AAGATC [also occurs]. Upstream regions of the cytokinin-regulated type-A ARRs showed the highest concentration of these motifs, generally clustering in the 500 bp proximal to the coding region. The sequence of this common upstream sequence motif closely matches (G/A)GAT(T/C), the optimal DNA-binding sequence identified in vitro for ARR1 and ARR2, two type-B ARRs (Sakai et al., 2000). Gel shift assays with various derivatives of the optimal type-B ARR-binding site NGAT(T/C) showed a slight preference for A at position 1 and a C at position 5, consistent with part of the common sequence motif we identified (Sakai et al., 2000). The frequency of this common upstream sequence motif in the upstream regions of the type-A ARRs is positively correlated with the level of their induction by cytokinin. The most highly cytokinin-induced genes, ARR5, ARR7, and ARR16, have multiple copies of this motif. Additionally, genes that are either only weakly induced by cytokinin or not expressed at detectable levels, ARR3, ARR4, and ARR17, have one or no motifs [...]. ARR6, which is moderately induced by cytokinin, does not fit this pattern because it has no consensus motif in its upstream region, although two such motifs are found within the fourth intron of this gene. The common upstream sequence motif (GATCTT) should randomly occur approximately 0.32 times per kilobase pair, taking into account the GC content observed in intergenic regions of Arabidopsis (approximately 33%). Our search of all genes present on the Affymetrix GeneChip that are expressed with a raw of at least 500 but not induced by cytokinin (950 genes) revealed that the sequence motif GATCTT is present a total of 358 times in the 1 kb upstream of the translational start site, or approximately 0.38 times per kilobase pair. In contrast, this core sequence motif is present 14 times among the upstream regions of the top 17 cytokinin up-regulated genes and only six times among the upstream regions of the 21 cytokinin down-regulated genes."[3]

Binding site for

Enhancer activity

Main article: Enhancer activity copy gene transcriptions

Promoter occurrences

Main article: Promoter occurrence gene transcriptions

Hypotheses

Main article: Hypotheses
  1. A1BG has no regulatory elements in either promoter.
  2. A1BG is not transcribed by a regulatory element.
  3. No regulatory element participates in the transcription of A1BG.

ARR1 Cytokinin samplings

Main article: Model samplings

Copying a responsive elements consensus sequence AGATT(C/T) and putting the sequence in "⌘F" finds one between ZNF497 and A1BG or one between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence AGATT(C/T) (starting with SuccessablesARR1.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 AGATT(C/T), 0.
  2. positive strand, negative direction, looking for AGATT(C/T), 1, AGATTC at 2452.
  3. positive strand, positive direction, looking for AGATT(C/T), 1, AGATTC at 122.
  4. negative strand, positive direction, looking for AGATT(C/T), 1, AGATTT at 2869.
  5. inverse complement, negative strand, negative direction, looking for (A/G)AATCT, 1, AAATCT at 50.
  6. inverse complement, positive strand, negative direction, looking for (A/G)AATCT, 0.
  7. inverse complement, positive strand, positive direction, looking for (A/G)AATCT, 0.
  8. inverse complement, negative strand, positive direction, looking for (A/G)AATCT, 2, GAATCT at 2725, GAATCT at 2243.

ARR1 distal promoters

Main article: Distal promoter gene transcriptions

Negative strand, negative direction: AAATCT at 50.

Positive strand, negative direction: AGATTC at 2452.

Negative strand, positive direction: AGATTT at 2869, GAATCT at 2725, GAATCT at 2243.

Positive strand, positive direction: AGATTC at 122.

ARR10 Cytokinin samplings

Main article: Model samplings

Copying a responsive elements consensus sequence (A/G)GATA(A/C)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 (A/G)GATA(A/C)G (starting with SuccessablesARR10.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)GATA(A/C)G, 0.
  2. positive strand, negative direction, looking for (A/G)GATA(A/C)G, 0.
  3. positive strand, positive direction, looking for (A/G)GATA(A/C)G, 0.
  4. negative strand, positive direction, looking for (A/G)GATA(A/C)G, 0.
  5. inverse complement, negative strand, negative direction, looking for C(G/T)TATC(C/T), 1, CGTATCC at 3447.
  6. inverse complement, positive strand, negative direction, looking for C(G/T)TATC(C/T), 0.
  7. inverse complement, positive strand, positive direction, looking for C(G/T)TATC(C/T), 0.
  8. inverse complement, negative strand, positive direction, looking for C(G/T)TATC(C/T), 0.

ARR10 UTRs

Main article: UTR promoter gene transcriptions

Negative strand, negative direction: CGTATCC at 3447.

ARR12 Cytokinin samplings

Main article: Model samplings

Copying a responsive elements consensus sequence (A/G)AGATA 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 (A/G)AGATA (starting with SuccessablesARR1.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)AGATA, 1, AAGATA at 1525.
  2. positive strand, negative direction, looking for (A/G)AGATA, 3, AAGATA at 2177, AAGATA at 1595, AAGATA at 57.
  3. positive strand, positive direction, looking for (A/G)AGATA, 0.
  4. negative strand, positive direction, looking for (A/G)AGATA, 0.
  5. inverse complement, negative strand, negative direction, looking for TATCT(C/T), 4, TATCTT at 4080, TATCTC at 1711, TATCTT at 356, TATCTT at 101.
  6. inverse complement, positive strand, negative direction, looking for TATCT(C/T), 1, TATCTT at 1732.
  7. inverse complement, positive strand, positive direction, looking for TATCT(C/T), 1, TATCTT at 2628.
  8. inverse complement, negative strand, positive direction, looking for TATCT(C/T), 0.

ARR12 UTRs

Main article: UTR promoter gene transcriptions

Negative strand, negative direction: TATCTT at 4080.

ARR12 distal promoters

Main article: Distal promoter gene transcriptions

Negative strand, negative direction: TATCTC at 1711, AAGATA at 1525, TATCTT at 356, TATCTT at 101.

Positive strand, negative direction: AAGATA at 2177, TATCTT at 1732, AAGATA at 1595, AAGATA at 57.

Positive strand, positive direction: TATCTT at 2628.

ARR (Ferreira) samplings

Main article: Model samplings

Copying a responsive elements consensus sequence (G/A)GGAT(T/C) and putting the sequence in "⌘F" finds one between ZNF497 and A1BG or three between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence (G/A)GGAT(T/C) (starting with SuccessablesARRF.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 (G/A)GGAT(T/C), 1, AGGATC at 2093.
  2. positive strand, negative direction, looking for (G/A)GGAT(T/C), 4, AGGATC at 4288, AGGATC at 4157, AGGATC at 4006, GGGATC at 2239.
  3. positive strand, positive direction, looking for (G/A)GGAT(T/C), 1, AGGATT at 2083.
  4. negative strand, positive direction, looking for (G/A)GGAT(T/C), 2, AGGATC at 4080, GGGATT at 2545.
  5. inverse complement, negative strand, negative direction, looking for (A/G)ATCC(C/T), 3, AATCCT at 3457, GATCCT at 1308, AATCCT at 239.
  6. inverse complement, positive strand, negative direction, looking for (A/G)ATCC(C/T), 13, GATCCC at 4477, AATCCC at 3976, AATCCC at 3067, AATCCC at 2678, AATCCT at 2091, AATCCC at 1917, GATCCC at 1814, AATCCC at 1782, AATCCC at 1264, AATCCC at 1137, AATCCC at 807, AATCCC at 673, AATCCC at 400.
  7. inverse complement, positive strand, positive direction, looking for (A/G)ATCC(C/T), 3, GATCCT at 4078, AATCCC at 2766, AATCCC at 2669.
  8. inverse complement, negative strand, positive direction, looking for (A/G)ATCC(C/T), 2, GATCCT at 2515, GATCCT at 2379.

ARRF UTRs

Main article: UTR promoter gene transcriptions

Negative strand, negative direction: AATCCT at 3457.

Positive strand, negative direction: GATCCC at 4477, AGGATC at 4288, AGGATC at 4157, AGGATC at 4006, AATCCC at 3976, AATCCC at 3067.

ARRF proximal promoters

Main article: Proximal promoter gene transcriptions

Positive strand, negative direction: AATCCC at 2678.

Negative strand, positive direction: AGGATC at 4080.

Positive strand, positive direction: GATCCT at 4078.

ARRF distal promoters

Main article: Distal promoter gene transcriptions

Negative strand, negative direction: AGGATC at 2093, GATCCT at 1308, AATCCT at 239.

Positive strand, negative direction: GGGATC at 2239, AATCCT at 2091, AATCCC at 1917, GATCCC at 1814, AATCCC at 1782, AATCCC at 1264, AATCCC at 1137, AATCCC at 807, AATCCC at 673, AATCCC at 400.

Negative strand, positive direction: GGGATT at 2545, GATCCT at 2515, GATCCT at 2379.

Positive strand, positive direction: AATCCC at 2766, AATCCC at 2669, AGGATT at 2083.

ARR (Rashotte1) samplings

Main article: Model samplings

Copying a responsive elements consensus sequence GATCTT and putting the sequence in "⌘F" finds one between ZNF497 and A1BG or three between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence GATCTT (starting with SuccessablesARRF.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 GATCTT, 0.
  2. positive strand, negative direction, looking for GATCTT, 0.
  3. positive strand, positive direction, looking for GATCTT, 1, GATCTT at 4066.
  4. negative strand, positive direction, looking for GATCTT, 0.
  5. inverse complement, negative strand, negative direction, looking for AAGATC, 0.
  6. inverse complement, positive strand, negative direction, looking for AAGATC, 2, AAGATC at 3276, AAGATC at 877.
  7. inverse complement, positive strand, positive direction, looking for AAGATC, 3, AAGATC at 4076, AAGATC at 4064, AAGATC at 2167.
  8. inverse complement, negative strand, positive direction, looking for AAGATC, 2, AAGATC at 964, AAGATC at 864.

ARRR1 UTRs

Main article: UTR promoter gene transcriptions

Positive strand, negative direction: AAGATC at 3276.

ARRR1 proximal promoters

Main article: Proximal promoter gene transcriptions

Positive strand, positive direction: AAGATC at 4076, AAGATC at 4064, GATCTT at 4066.

ARRR1 distal promoters

Main article: Distal promoter gene transcriptions

Positive strand, negative direction: AAGATC at 877.

Negative strand, positive direction: AAGATC at 964, AAGATC at 864.

Positive strand, positive direction: AAGATC at 2167.

ARR (Rashotte2) samplings

Main article: Model samplings

Copying a responsive elements consensus sequence (G/A)GAT(T/C) and putting the sequence in "⌘F" finds one between ZNF497 and A1BG or three between ZSCAN22 and A1BG as can be found by the computer programs.

For the Basic programs testing consensus sequence (G/A)GAT(T/C) (starting with SuccessablesARRF.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 (G/A)GAT(T/C), 5, GGATC at 2093, GGATT at 1591, GGATC at 1306, GGATT at 64, AGATT at 9.
  2. positive strand, negative direction, looking for (G/A)GAT(T/C), 24, AGATC at 4475, GGATC at 4288, GGATC at 4157, GGATC at 4006, AGATC at 3488, AGATC at 3276, GGATC at 3097, GGATC at 2574, AGATT at 2451, AGATC at 2413, GGATC at 2239, AGATC at 1987, GGATC at 1812, AGATT at 1714, AGATT at 1334, GGATC at 1167, AGATT at 1043, AGATC at 972, AGATC at 877, GGATC at 703, AGATC at 589, AGATT at 583, GGATC at 525, GGATC at 430.
  3. positive strand, positive direction, looking for (G/A)GAT(T/C), 6, AGATC at 4076, AGATC at 4064, GGATC at 2481, AGATC at 2167, GGATT at 2083, AGATT at 121.
  4. negative strand, positive direction, looking for (G/A)GAT(T/C), 6, GGATC at 4080, AGATT at 2868, GGATT at 2545, AGATC at 2230, AGATC at 964, AGATC at 864.
  5. inverse complement, negative strand, negative direction, looking for (A/G)ATC(C/T), 7, GATCT at 3463, AATCC at 3456, AATCT at 3000, AATCT at 2979, GATCC at 1307, AATCC at 238, AATCT at 50.
  6. inverse complement, positive strand, negative direction, looking for (A/G)ATC(C/T), 17, GATCC at 4476, AATCC at 3975, AATCC at 3679, AATCC at 3066, AATCC at 2677, AATCC at 2090, AATCC at 1916, GATCC at 1813, AATCC at 1781, GATCT at 1482, AATCC at 1263, AATCC at 1136, GATCC at 973, AATCC at 806, AATCC at 672, AATCC at 399, AATCT at 232.
  7. inverse complement, positive strand, positive direction, looking for (A/G)ATC(C/T), 10, GATCC at 4077, GATCT at 4065, GATCC at 3522, GATCC at 3484, AATCC at 2765, AATCC at 2668, GATCC at 2639, GATCC at 2482, AATCC at 2366, AATCC at 150.
  8. inverse complement, negative strand, positive direction, looking for (A/G)ATC(C/T), 9, GATCC at 4081, AATCC at 3797, AATCT at 2725, GATCC at 2514, GATCC at 2378, AATCT at 2243, AATCT at 2235, GATCC at 965, GATCC at 865.

ARRR2 UTRs

Main article: UTR promoter gene transcriptions

Negative strand, negative direction: GATCT at 3463, AATCC at 3456, AATCT at 3000, AATCT at 2979.

Positive strand, negative direction: GATCC at 4476, AGATC at 4475, GGATC at 4288, GGATC at 4157, GGATC at 4006, AATCC at 3975, AATCC at 3679, AGATC at 3488, AGATC at 3276, GGATC at 3097, AATCC at 3066.

ARRR2 proximal promoters

Main article: Proximal promoter gene transcriptions

Positive strand, negative direction: AATCC at 2677.

Negative strand, positive direction: GATCC at 4081, GGATC at 4080.

Positive strand, positive direction: GATCC at 4077, AGATC at 4076, GATCT at 4065, AGATC at 4064.

ARRR2 distal promoters

Main article: Distal promoter gene transcriptions

Negative strand, negative direction: GGATC at 2093, GGATT at 1591, GATCC at 1307, GGATC at 1306, AATCC at 238, GGATT at 64, AATCT at 50, AGATT at 9.

Positive strand, negative direction: GGATC at 2574, AGATT at 2451, AGATC at 2413, GGATC at 2239, AATCC at 2090, AGATC at 1987, AATCC at 1916, GATCC at 1813, GGATC at 1812, AATCC at 1781, AGATT at 1714, GATCT at 1482, AGATT at 1334, AATCC at 1263, GGATC at 1167, AATCC at 1136, AGATT at 1043, GATCC at 973, AGATC at 972, AGATC at 877, AATCC at 806, GGATC at 703, AATCC at 672, AGATC at 589, AGATT at 583, GGATC at 525, GGATC at 430, AATCC at 399, AATCT at 232.

Negative strand, positive direction: AATCC at 3797, AGATT at 2868, AATCT at 2725, GGATT at 2545, GATCC at 2514, GATCC at 2378, AATCT at 2243, AATCT at 2235, AGATC at 2230, GATCC at 965, AGATC at 964, GATCC at 865, AGATC at 864.

Positive strand, positive direction: GATCC at 3522, GATCC at 3484, AATCC at 2765, AATCC at 2668, GATCC at 2639, GATCC at 2482, GGATC at 2481, AATCC at 2366, AGATC at 2167, GGATT at 2083, AATCC at 150, AGATT at 121.

Acknowledgements

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

See also

References

  1. ↑ 1.0 1.1 1.2 1.3 Mingtang Xie1, Hongyu Chen, Ling Huang, Ryan C. O’Neil1, Maxim N. Shokhirev & Joseph R. Ecker (23 April 2018). "A B-ARR-mediated cytokinin transcriptional network directs hormone cross-regulation and shoot development" (PDF). Nature Communications. 9 (1604): 1–13. doi:10.1038/s41467-018-03921-6. Retrieved 26 April 2021.
  2. ↑ 2.0 2.1 2.2 2.3 Fernando J Ferreira and Joseph J Kieber (October 2005). "Cytokinin signaling" (PDF). Current Opinion in Plant Biology. 8 (5): 518–525. doi:10.1016/j.pbi.2005.07.013. Retrieved 28 April 2021.
  3. ↑ 3.0 3.1 Aaron M. Rashotte, Susan D.B. Carson, Jennifer P.C. To, and Joseph J. Kieber (August 2003). "Expression Profiling of Cytokinin Action in Arabidopsis" (PDF). Plant Physiology. 132 (4): 1998–2011. doi:10.1104/pp.103.021436. Retrieved 28 April 2021.

External links

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