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Gene transcriptions/Boxes/Ws

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Arabis neglecta habitat is Tatra Mountains, Orla Perć, Kozia Przełęcz. Credit: Jerzy Opioła.{{free media}}

"Consistent with its role as a transcriptional repressor, OsWRKY71 binds specifically to functionally defined TGAC-containing W boxes of the Amy32b promoter in electrophoretic mobility shift assays (Zhang et al. 2004)."[1]

"Details of auto-regulation or cross-regulation by WRKY factors were provided for the parsley group I member PcWRKY1 and its ortholog AtWRKY33 [37**,39,41]. In response to PAMP treatment PcWRKY1 transcripts accumulate rapidly and transiently [42]. AtWRKY33 is activated with similar kinetics by defense-related stimuli [18,34,41]. This rapid response is mediated by a conserved arrangement of three synergistically acting W boxes (WABC). Chromatin immunoprecipitation (ChIP) revealed that in vivo these orthologous W boxes are constitutively occupied by WRKY proteins [37**,41]."[2]

"The synthesis of SA and the expression of NPR1, a key regulator of some PAMP-triggered responses, appear to be partly controlled by WRKY factors. NPR1 is regulated by WRKY TFs interacting with two W box elements in its 50UTR [44]. Defense-associated SA production is strongly dependent on pathogen-inducible expression of ICS1 [45]. This gene is a likely target of WRKY TFs, as its promoter is enriched for W boxes."[2]

A "missense mutation within its WRKY domain results in conditional activation of defense responses and loss of in vitro binding to W boxes suggesting a negative role of this factor in defense signaling [49]."[2]

Functionality and conservation of the W-box element across plant species shown by gel shift experiments, random binding site selection, yeast one-hybrid screens and co-transfection assays performed with many different WRKY proteins and In silico-based studies have identified clusters of W-boxes in stress-inducible promoters, where the binding of WRKY proteins to W-boxes is a feature of both biotic and abiotic stress responses, together with other plant processes such as germination.[3] It has also been shown that multiple W-boxes have a synergistic effect on transcription.[3]

Almost all WRKY transcription factors bind preferentially to W-boxes, and since their discovery, this has raised the question as to how they show specificity for the promoters of their target genes.[4] Although the W-box core is required, adjacent sequences also play a role in determining binding-site preference.[5] Recent evidence suggests that the TGAC core is more degenerate, composed of a guanine adenine cytosine (GAC) core, and the upstream thymine and downstream pyrimidine flanking sequences help dictate recognition by specific WRKY factors.[6] Basic residues of the WRKY protein domain also are believed to recognize the phosphate backbone of the cis-element.[6]

The solution structure of the C-terminal WRKY domain of Arabidopsis WRKY4 in complex with the W-box DNA has been determined by NMR.[7] A four-stranded β-sheet enters the major groove of DNA in a structure called the β-wedge, where the sheet is nearly perpendicular to the DNA helical ais: as predicted amino acids in the conserved WRKYGQK signature motif contact the W-box DNA.[7]

WRKY

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WRKY family of genes contain the common degenerate nucleotide sequence: WRKY, or W = A or T (U) [Weak], R = A or G [puRine], K = G or T (U) [Keto], Y = C or T (U) [pYrimidine].

"Plant immune responses are associated with the concerted modulation of a large number of different WRKY transcripts and proteins [15,34–36,37**]. Upon triggering of SA-dependent defenses, at least 49 AtWRKY genes exhibited differential regulation representing separate waves of transcript accumulation or repression [34]. Their promoters are statistically enriched for W boxes, suggesting that they are autoregulated or controlled by other WRKY proteins [34]."[2]

"Some architectural features of the WRKY web are emerging. As motif D containing group I WRKY TFs can be phosphorylated by MAP-kinases, they are likely to serve as the first WRKY proteins activated in response to PAMP-triggered MAPK signaling. Their targets may include the IIe WRKY genes AtWRKY22 and AtWRKY29, which are upregulated by a PAMP-induced MAPK cascade and contain multiple W boxes within their respective promoters [4]."[2]

Consensus sequences

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The "presence of WRKY TF binding sites (C/TTGACC/T, W boxes) in numerous co-regulated Arabidopsis defense gene promoters provided circumstantial evidence that zinc-finger-type WRKY factors play a broad and pivotal role in regulating defenses [10]."[2]

The W box is a DNA cis-regulatory element sequence, (T)TGAC(C/T), which is recognized by the family of WRKY transcription factors.[8][4]

Sampling A1BG promoters

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For the Basic programs (starting with SuccessablesWbox.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 (+), including extending the number of nts from 958 to 4445, the programs are, are looking for, and found:

  1. negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesWbox--.bas, looking for 3'-(C/T)TGAC(C/T)-5', 5, 3'-CTGACT-5', 17, 3'-TTGACT-5', 130, 3'-TTGACT-5', 307, 3'-CTGACT-5', 1935, 3'-CTGACC-5', 3749,
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesWbox-+.bas, looking for 3'-(C/T)TGAC(C/T)-5', 6, 3'-CTGACC-5', 1662, 3'-CTGACC-5', 2213, 3'-TTGACC-5', 2873, 3'-CTGACT-5', 2945, 3'-TTGACC-5', 4018, 3'-CTGACC-5', 4216,
  3. positive strand in the negative direction is SuccessablesWbox+-.bas, looking for 3'-(C/T)TGAC(C/T)-5', 1, 3'-CTGACC-5', 734,
  4. positive strand in the positive direction is SuccessablesWbox++.bas, looking for 3'-(C/T)TGAC(C/T)-5', 3, 3'-TTGACC-5', 1953, 3'-CTGACT-5', 2674, 3'-TTGACT-5', 3735,
  5. complement, negative strand, negative direction is SuccessablesWboxc--.bas, looking for 3'-(A/G)ACTG(A/G)-5', 1, 3'-GACTGG-5', 734,
  6. complement, negative strand, positive direction is SuccessablesWboxc-+.bas, looking for 3'-(A/G)ACTG(A/G)-5', 3, 3'-AACTGG-5', 1953, 3'-GACTGA-5', 2674, 3'-AACTGA-5', 3735,
  7. complement, positive strand, negative direction is SuccessablesWboxc+-.bas, looking for 3'-(A/G)ACTG(A/G)-5', 5, 3'-GACTGA-5', 17, 3'-AACTGA-5', 130, 3'-AACTGA-5', 307, 3'-GACTGA-5', 1935, 3'-GACTGG-5', 3749,
  8. complement, positive strand, positive direction is SuccessablesWboxc++.bas, looking for 3'-(A/G)ACTG(A/G)-5', 6, 3'-GACTGG-5', 1662, 3'-GACTGG-5', 2213, 3'-AACTGG-5', 2873, 3'-GACTGA-5', 2945, 3'-AACTGG-5', 4018, 3'-GACTGG-5', 4216,
  9. inverse complement, negative strand, negative direction is SuccessablesWboxci--.bas, looking for 3'-(A/G)GTCA(A/G)-5', 2, 3'-GGTCAG-5', 1353, 3'-GGTCAA-5', 4416,
  10. inverse complement, negative strand, positive direction is SuccessablesWboxci-+.bas, looking for 3'-(A/G)GTCA(A/G)-5', 6, 3'-AGTCAG-5', 2101, 3'-GGTCAG-5', 2221, 3'-AGTCAG-5', 2608, 3'-AGTCAA-5', 2614, 3'-AGTCAG-5', 2619, 3'-GGTCAG-5', 4270,
  11. inverse complement, positive strand, negative direction is SuccessablesWboxci+-.bas, looking for 3'-(A/G)GTCA(A/G)-5', 6, 3'-GGTCAG-5', 440, 3'-GGTCAG-5', 577, 3'-GGTCAG-5', 713, 3'-GGTCAG-5', 2249, 3'-GGTCAG-5', 2586, 3'-GGTCAA-5', 4308,
  12. inverse complement, positive strand, positive direction is SuccessablesWboxci++.bas, looking for 3'-(A/G)GTCA(A/G)-5', 6, 3'-GGTCAG-5', 2025, 3'-AGTCAG-5', 2099, 3'-GGTCAG-5', 2606, 3'-GGTCAG-5', 2997, 3'-GGTCAG-5', 3083, 3'-GGTCAA-5', 3380,
  13. inverse, negative strand, negative direction, is SuccessablesWboxi--.bas, looking for 3'-(C/T)CAGT(C/T)-5', 6, 3'-CCAGTC-5', 440, 3'-CCAGTC-5', 577, 3'-CCAGTC-5', 713, 3'-CCAGTC-5', 2249, 3'-CCAGTC-5', 2586, 3'-CCAGTT-5', 4308,
  14. inverse, negative strand, positive direction, is SuccessablesWboxi-+.bas, looking for 3'-(C/T)CAGT(C/T)-5', 6, 3'-CCAGTC-5', 2025, 3'-TCAGTC-5', 2099, 3'-CCAGTC-5', 2606, 3'-CCAGTC-5', 2997, 3'-CCAGTC-5', 3083, 3'-CCAGTT-5', 3380,
  15. inverse, positive strand, negative direction, is SuccessablesWboxi+-.bas, looking for 3'-(C/T)CAGT(C/T)-5', 2, 3'-CCAGTC-5', 1353, 3'-CCAGTT-5', 4416,
  16. inverse, positive strand, positive direction, is SuccessablesWboxi++.bas, looking for 3'-(C/T)CAGT(C/T)-5', 6, 3'-TCAGTC-5', 2101, 3'-CCAGTC-5', 2221, 3'-TCAGTC-5', 2608, 3'-TCAGTT-5', 2614, 3'-TCAGTC-5', 2619, 3'-CCAGTC-5', 4270.

See also

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References

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  1. ↑ Liu-Min Fan, Xiaoyan Feng, Yu Wang and Xing Wang Deng (2007). "Gibberellin Signal Transduction in Rice". Journal of Integrative Plant Biology 49 (6): 731−741. doi:10.1111/j.1744-7909.2007.00511.x. https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1744-7909.2007.00511.x. Retrieved 16 October 2018. 
  2. ↑ 2.0 2.1 2.2 2.3 2.4 2.5 Thomas Eulgem and Imre E Somssich (2007). "Networks of WRKY transcription factors in defense signaling". Current Opinion in Plant Biology 10: 366–371. doi:10.1016/j.pbi.2007.04.020. http://pubman.mpdl.mpg.de/pubman/item/escidoc:1221669/component/escidoc:1221668/eulgem_curr_op_plant_biol_2007.pdf. Retrieved 17 October 2018. 
  3. ↑ 3.0 3.1 Rushton, Paul. The Lab of Dr. Paul Rushton. wordpress.com. http://therushtonlab.wordpress.com/. Retrieved 17 June 2013. 
  4. ↑ 4.0 4.1 "WRKY transcription factors". Trends Plant Science 15 (5): 247–58. May 2010. doi:10.1016/j.tplants.2010.02.006. PMID 20304701. 
  5. ↑ Ciolkowski, I.; Wanke D; Birkenbihl RP; Somssich IE. (2008). "Studies on DNA-binding selectivity of WRKY transcription factors lend structural clues into WRKY-domain function". Plant Mol Biol. 68: 81–92. doi:10.1007/s11103-008-9353-1. PMID 18523729. PMC 2493524. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2493524/. 
  6. ↑ 6.0 6.1 Brand; Fischer; Harter; Kohlbacher; Wanke (2013). "Elucidating the evolutionary conserved DNA-binding specificities of WRKY transcription factors by molecular dynamics and in vitro binding assays". Nucleic Acids Research 41 (21): 9764–9778. doi:10.1093/nar/gkt732. 
  7. ↑ 7.0 7.1 Yamasaki, K.; Kigawa T; Watanabe S; Inoue M; Yamasaki T; Seki M; Shinozaki K; Yokoyama S. (2012). "Structural basis for sequence-specific DNA recognition by an Arabidopsis WRKY transcription factor". J. Biol. Chem. 287: 7683–91. doi:10.1074/jbc.M111.279844. PMID 22219184. PMC 3293589. //www.ncbi.nlm.nih.gov/pmc/articles/PMC3293589/. 
  8. ↑ Rushton, Paul; Macdonald, H.; Huttly, A.K.; Lazarus, C.M.; Hooley, R (1995). "Members of a new family of DNA-binding proteins bind to a conserved cis-element in the promoters of alpha-Amy2 genes". Plant Molecular Biology 29: 691–702. doi:10.1007/bf00041160. PMID 8541496. 
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