Whirly Genomic sequences

Minimum number of tobacco Whirly genes: 2

Count of tobacco Whirly sequences: 4

Pfam accession: Plant_TF

SHOULD possess Plant_TF domain

Members of the Whirly family of proteins are found throughout the plant kingdom and are predicted to share the ability to bind to single-stranded DNA. Arabidopsis and potato Whirly orthologs act as transcription factors that regulate defense gene expression; the Arabidopsis Whirly protein AtWhy1 contributes to both basal and specific defense responses. Analysis of the crystal structure of potato StWhy1 has provided insight into the DNA-binding mechanism of this family of proteins, their mode of action and possible autoregulation. There is evidence to suggest that Whirly proteins might play roles in processes other than defense responses and could function in the chloroplast as well as in the nucleus.

This Whirly family is also named PBF-2-like family.

Elicitor-induced activation of the potato pathogenesis-related gene PR-10a requires a 30-bp promoter sequence termed the ERE (elicitor response element) that is bound by the nuclear factor PBF-2 (PR-10a binding factor 2). In this study, PBF-2 has been purified to near homogeneity from elicited tubers through a combination of anion-exchange and DNA affinity chromatography. Evidence demonstrates that inactive PBF-2 is stored in the nuclei of fresh tubers and becomes available for binding to the ERE upon elicitation. A protein with an apparent molecular mass of 24 kD (p24) is a DNA binding component of PBF-2. A cDNA encoding p24 has been cloned and encodes a novel protein with a potential transcriptional activation domain that could also act as a single-stranded DNA binding domain. Both PBF-2 and the cDNA-encoded protein bind with high affinity to the single-stranded form of the ERE in a sequence-specific manner. The inverted repeat sequence of the ERE, TGACAnnnnTGTCA, is critical for binding of this factor in vitro and for PR-10a expression in vivo, supporting the role of PBF-2 as a transcriptional regulator.


Desveaux, D; Allard, J; Brisson, N; Sygusch, J. A new family of plant transcription factors displays a novel ssDNA-binding surface. Nat. Struct. Biol. 2002. 9(7):512-7 PMID: 12080340

Desveaux, D; Després, C; Joyeux, A; Subramaniam, R; Brisson, N. PBF-2 is a novel single-stranded DNA binding factor implicated in PR-10a gene activation in potato. Plant Cell 2000. 12(8):1477-89 PMID: 10948264

Desveaux, D; Maréchal, A; Brisson, N. Whirly transcription factors: defense gene regulation and beyond. Trends Plant Sci. 2005. 10(2):95-102 PMID: 15708347

Number of contigs: 2

Number of singlets: 2

Number of N terminal – 1

Number of C terminal – 1

Number of genes with N terminal and middle part of domain – 1

Number of genes with middle part of domain – 1

Total minimum number – 2

Search sequences and info

Transcription factor sequences
Whirly_1 [comment=5 prime end] ET043206
Whirly_2 [comment=5 prime end and middle] ET049879
Whirly_3 [comment=middle] ET045707
Whirly_4 [comment=3 prime end] ET044107

Tobacco published genes related to transcription factor family Whirly
Family Genbank ID Name
Authors of this site:

Paul J Rushton
Marta T. Bokowiec
Xianfeng (Jeff) Chen
Thomas (Tom) W Laudeman
Jennifer F. Brannock
Michael P. Timko