W box gene transcriptions: Difference between revisions

Jump to navigation Jump to search
VisualWikitext
Line 111: Line 111:
==W box random dataset samplings==
==W box random dataset samplings==


# RDr0: 0.
# Wboxr0: 6, TTGACC at 4380, TTGACT at 4031, CTGACT at 3270, CTGACC at 1834, CTGACC at 1659, TTGACT at 231.
# RDr1: 0.
# Wboxr1: 5, TTGACT at 4021, TTGACC at 3051, TTGACT at 2937, CTGACC at 1160, CTGACC at 154.
# RDr2: 0.
# RDr2: 0.
# RDr3: 0.
# RDr3: 0.
Line 132: Line 132:
# RDr9ci: 0.
# RDr9ci: 0.


===RDr arbitrary (evens) (4560-2846) UTRs===
===Wboxr arbitrary (evens) (4560-2846) UTRs===


===RDr alternate (odds) (4560-2846) UTRs===
# Wboxr0: TTGACC at 4380, TTGACT at 4031, CTGACT at 3270.
 
===Wboxr alternate (odds) (4560-2846) UTRs===
 
# Wboxr1: TTGACT at 4021, TTGACC at 3051, TTGACT at 2937.


===RDr arbitrary negative direction (evens) (2846-2811) core promoters===
===RDr arbitrary negative direction (evens) (2846-2811) core promoters===


===RDr alternate negative direction (odds) (2846-2811) core promoters===
===RDr alternate negative direction (odds) (2846-2811) core promoters===


===RDr arbitrary positive direction (odds) (4445-4265) core promoters===
===RDr arbitrary positive direction (odds) (4445-4265) core promoters===


===RDr alternate positive direction (evens) (4445-4265) core promoters===
===Wboxr alternate positive direction (evens) (4445-4265) core promoters===
 
# Wboxr0: TTGACC at 4380.
 
===Wboxr arbitrary negative direction (evens) (2811-2596) proximal promoters===


===RDr arbitrary negative direction (evens) (2811-2596) proximal promoters===


===RDr alternate negative direction (odds) (2811-2596) proximal promoters===
===RDr alternate negative direction (odds) (2811-2596) proximal promoters===


===RDr arbitrary positive direction (odds) (4265-4050) proximal promoters===
===RDr arbitrary positive direction (odds) (4265-4050) proximal promoters===


===RDr alternate positive direction (evens) (4265-4050) proximal promoters===
===RDr alternate positive direction (evens) (4265-4050) proximal promoters===


===RDr arbitrary negative direction (evens) (2596-1) distal promoters===


===RDr alternate negative direction (odds) (2596-1) distal promoters===
===Wboxr arbitrary negative direction (evens) (2596-1) distal promoters===
 
# Wboxr0: CTGACC at 1834, CTGACC at 1659, TTGACT at 231.
 
===Wboxr alternate negative direction (odds) (2596-1) distal promoters===
 
# Wboxr1: CTGACC at 1160, CTGACC at 154.
 
===Wboxr arbitrary positive direction (odds) (4050-1) distal promoters===
 
# Wboxr1: TTGACT at 4021, TTGACC at 3051, TTGACT at 2937, CTGACC at 1160, CTGACC at 154.


===RDr arbitrary positive direction (odds) (4050-1) distal promoters===
===Wboxr alternate positive direction (evens) (4050-1) distal promoters===


===RDr alternate positive direction (evens) (4050-1) distal promoters===
# Wboxr0: TTGACT at 4031, CTGACT at 3270, CTGACC at 1834, CTGACC at 1659, TTGACT at 231.


==Wbox analysis and results==
==Wbox analysis and results==

Revision as of 05:49, 19 March 2023

Editor-In-Chief: Henry A. Hoff

File:Arabis neglecta a1.jpg
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

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

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]

W box samplings

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. positive strand in the negative direction is SuccessablesWbox+-.bas, looking for 3'-(C/T)TGAC(C/T)-5', 1, 3'-CTGACC-5', 734,
  3. 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,
  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.

Wbox (4560-2846) UTRs

  1. Negative strand, negative direction: CTGACC at 3749.
  2. Negative strand, negative direction: GGTCAA at 4416.
  3. Positive strand, negative direction: GGTCAA at 4308.

Wbox positive direction (4445-4265) core promoters

  1. Negative strand, positive direction: GGTCAG at 4270.

Wbox positive direction (4265-4050) proximal promoters

  1. Negative strand, positive direction: CTGACC at 4216.

Wbox negative direction (2596-1) distal promoters

  1. Negative strand, negative direction: CTGACT at 1935, TTGACT at 307, TTGACT at 130, CTGACT at 17.
  2. Negative strand, negative direction: GGTCAG at 1353.
  3. Positive strand, negative direction: CTGACC at 734.
  4. Positive strand, negative direction: GGTCAG at 2586, GGTCAG at 2249, GGTCAG at 713, GGTCAG at 577, GGTCAG at 440.

Wbox positive direction (4050-1) distal promoters

  1. Negative strand, positive direction: TTGACC at 4018, CTGACT at 2945, TTGACC at 2873, CTGACC at 2213, CTGACC at 1662.
  2. Negative strand, positive direction: AGTCAG at 2619, AGTCAA at 2614, AGTCAG at 2608, GGTCAG at 2221, AGTCAG at 2101.
  3. Positive strand, positive direction: TTGACT at 3735, CTGACT at 2674, TTGACC at 1953.
  4. Positive strand, positive direction: GGTCAA at 3380, GGTCAG at 3083, GGTCAG at 2997, GGTCAG at 2606, AGTCAG at 2099, GGTCAG at 2025.

W box random dataset samplings

  1. Wboxr0: 6, TTGACC at 4380, TTGACT at 4031, CTGACT at 3270, CTGACC at 1834, CTGACC at 1659, TTGACT at 231.
  2. Wboxr1: 5, TTGACT at 4021, TTGACC at 3051, TTGACT at 2937, CTGACC at 1160, CTGACC at 154.
  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.

Wboxr arbitrary (evens) (4560-2846) UTRs

  1. Wboxr0: TTGACC at 4380, TTGACT at 4031, CTGACT at 3270.

Wboxr alternate (odds) (4560-2846) UTRs

  1. Wboxr1: TTGACT at 4021, TTGACC at 3051, TTGACT at 2937.

RDr arbitrary negative direction (evens) (2846-2811) core promoters

RDr alternate negative direction (odds) (2846-2811) core promoters

RDr arbitrary positive direction (odds) (4445-4265) core promoters

Wboxr alternate positive direction (evens) (4445-4265) core promoters

  1. Wboxr0: TTGACC at 4380.

Wboxr arbitrary negative direction (evens) (2811-2596) proximal promoters

RDr alternate negative direction (odds) (2811-2596) proximal promoters

RDr arbitrary positive direction (odds) (4265-4050) proximal promoters

RDr alternate positive direction (evens) (4265-4050) proximal promoters

Wboxr arbitrary negative direction (evens) (2596-1) distal promoters

  1. Wboxr0: CTGACC at 1834, CTGACC at 1659, TTGACT at 231.

Wboxr alternate negative direction (odds) (2596-1) distal promoters

  1. Wboxr1: CTGACC at 1160, CTGACC at 154.

Wboxr arbitrary positive direction (odds) (4050-1) distal promoters

  1. Wboxr1: TTGACT at 4021, TTGACC at 3051, TTGACT at 2937, CTGACC at 1160, CTGACC at 154.

Wboxr alternate positive direction (evens) (4050-1) distal promoters

  1. Wboxr0: TTGACT at 4031, CTGACT at 3270, CTGACC at 1834, CTGACC at 1659, TTGACT at 231.

Wbox analysis and results

Main article: Complex locus A1BG and ZNF497 § Wboxes

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]

Reals or randoms Promoters direction Numbers Strands Occurrences Averages (± 0.1)
Reals UTR negative 3 2 1.5 1.5 ± 0.5 (--2,+-1)
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 arbitrary negative 0 10 0 0
Randoms Core alternate negative 0 10 0 0
Reals Core positive 1 2 0.5 0.5
Randoms Core arbitrary positive 0 10 0 0
Randoms Core alternate positive 0 10 0 0
Reals Proximal negative 0 2 0 0
Randoms Proximal arbitrary negative 0 10 0 0
Randoms Proximal alternate negative 0 10 0 0
Reals Proximal positive 1 2 0.5 0.5
Randoms Proximal arbitrary positive 0 10 0 0
Randoms Proximal alternate positive 0 10 0 0
Reals Distal negative 11 2 5.5 5.5 ± 0.5 (--5,+-6)
Randoms Distal arbitrary negative 0 10 0 0
Randoms Distal alternate negative 0 10 0 0
Reals Distal positive 19 2 9.5 9.5 ± 0.5 (-+10,++9)
Randoms Distal arbitrary positive 0 10 0 0
Randoms Distal alternate positive 0 10 0 0

Comparison:

The occurrences of real Wboxes are greater than the randoms. This suggests that the real Wboxes are likely active or activable.

Acknowledgements

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

Initial content for this page in some instances came from Wikiversity.

See also

References

  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. Retrieved 16 October 2018.
  2. ↑ 2.0 2.1 2.2 2.3 2.4 2.5 2.6 Thomas Eulgem and Imre E Somssich (2007). "Networks of WRKY transcription factors in defense signaling" (PDF). Current Opinion in Plant Biology. 10: 366–371. doi:10.1016/j.pbi.2007.04.020. Retrieved 17 October 2018.
  3. ↑ 3.0 3.1 Rushton, Paul. The Lab of Dr. Paul Rushton. wordpress.com. Retrieved 17 June 2013.
  4. ↑ 4.0 4.1 Rushton PJ, Somssich IE, Ringler P, Shen QJ (May 2010). "WRKY transcription factors". Trends Plant Science. 15 (5): 247–58. 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. PMC 2493524. PMID 18523729.
  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. PMC 3293589. PMID 22219184.
  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.

External links

Retrieved from "https://www.wikidoc.org/index.php?title=W_box_gene_transcriptions&oldid=1733384"