The B3 Superfamily of Plant Transcription Factors

The B3 superfamily of Transcription Factors has only been reported in the Viridiplantae kingdom from Chlorophyta to gymnosperms and angiosperms. Several phylogenetic analysis of the B3 superfamily distinguish between four to five structural families.
The ARF, REV, REM and LAV (which can be subdivided into VAL and ABI3/LEC2) or the ARF, REV, REM, VAL/HSI and ABI3/LEC2 (PMID:18986826 ; 22302388 ; 19503786 ; 23377560). The B3 superfamily appears to have evolved via gene duplication from a single lineage, as observed today in Chlorophyta, with the most “ancient” model exhibiting similarity to the VAL/HSI gene family in multicellular plants.

B3 families can be described with clear rules combining required and forbidden protein domains.
ARF family: Contains B3 and the Auxin Response Factor domains.
REV family: Contains B3 and AP2 domains.
REM family: Contains several copies of the B3 domain forbidden domains are Auxin Response Factor, AP2 and CW-type Zinc Finger
VAL/HSI family: Contains B3 domain and a CW-type Zinc Finger domain at the C-terminus.
ABI3/LEC2 family: Contains one B3 domain forbidden domains are Auxin Response Factor, AP2 and CW-type Zinc Finger

The B3 binding domain interacts with the major groove of DNA (PMID: 15548737). However, not much is known about the cis-element recognized in each of the families. Some particular preferences are know, for instance the maize VP1 is capable of recognizes the Sph box at the C1 promoter (PMID: 9165754). In rice a member of this family is related to the iron (Fe) deficiency response by binding the IDE1 cis-element (PMID: 19737364). The IRON DEFICIENCY RESPONSIVE CIS-ACTING ELEMENT BIDING FACTOR 1 (IDEF1) gene is expressed in constitutively expressed during both vegetative and reproductive stages (PMID: 20197292). Additionally IDEF1 is able to regulate by binding to the RY element when participating of seed development regulation.

I have estimated gene content in each of the currently available monocots genomes and basically I am looking for contrasting my results with the studies previously done in dictos where others have suggested a non uniform amplification of the B3 superfamily (i.e., not all the families have equally expanded).

My notes about Brassinosteroid Signaling Network

Crystal structure of BAK1 phosphorylated cytoplasmic domain (CD) in complex with AMP-PNP as found in Arabidopsis thaliana
Yan L, Ma Y, Liu D, Wei X, Sun Y, Chen X, Zhao H, Zhou J, Wang Z, Shui W, Lou Z. 2012. Structural basis for the impact of phosphorylation on the activation of plant receptor-like kinase BAK1. Cell Res. 22(8):1304-8. doi: 10.1038/cr.2012.74

Brassinosteroid (BR) Gene Regulatory Network :

1. Sun, Y. et al. Integration of brassinosteroid signal transduction with the transcription network for plant growth regulation in Arabidopsis. Developmental Cell 19, 765–777 (2010).
2. Cheminant, S. et al. DELLAs regulate chlorophyll and carotenoid biosynthesis to prevent photooxidative damage during seedling deetiolation in Arabidopsis. Plant Cell 23, 1849–1860 (2011).
3. Ye, H., Li, L., Guo, H. & Yin, Y. MYBL2 is a substrate of GSK3-like kinase BIN2 and acts as a corepressor of BES1 in brassinosteroid signaling pathway in Arabidopsis. Proc. Natl. Acad. Sci. U.S.A. 109, 20142–20147 (2012).
4. Wang, Z.-Y., Bai, M.-Y., Oh, E. & Zhu, J.-Y. Brassinosteroid signaling network and regulation of photomorphogenesis. Annu. Rev. Genet. 46, 701–724 (2012).
5. Oh, M.-H., Wang, X., Clouse, S. D. & Huber, S. C. Deactivation of the Arabidopsis BRASSINOSTEROID INSENSITIVE 1 (BRI1) receptor kinase by autophosphorylation within the glycine-rich loop. Proc. Natl. Acad. Sci. U.S.A. 109, 327–332 (2012).
6. Oh, E., Zhu, J.-Y. & Wang, Z.-Y. Interaction between BZR1 and PIF4 integrates brassinosteroid and environmental responses. Nat. Cell Biol. 14, 802–809 (2012).
7. Kumar, S. V. et al. Transcription factor PIF4 controls the thermosensory activation of flowering. Nature 484, 242–245 (2012).
8. Bai, M.-Y. et al. Brassinosteroid, gibberellin and phytochrome impinge on a common transcription module in Arabidopsis. Nat. Cell Biol. 14, 810–817 (2012).
9. Daviere, J. M. & Achard, P. Gibberellin signaling in plants. Development 140, 1147–1151 (2013).
10. Sakamoto, T., Morinaka, Y., Inukai, Y., Kitano, H. & Fujioka, S. Auxin signal transcription factor regulates expression of the brassinosteroid receptor gene in rice. Plant J. 73, 676–688 (2013).

Plus two bonus from December, 2013

11.  Zhang, D et al., Transcription factor HAT1 is phosphorylated by BIN2 kinase and mediates brassinosteroid repressed gene expression in Arabidopsis. Plant J. (2013).
12. Cheon J, Fujioka S, Dilkes BP, Choe S. Brassinosteroids Regulate Plant Growth through Distinct Signaling Pathways in Selaginella and Arabidopsis. PLoS One. 8(12):e81938 (2013).

BTW, the last paper [reference 12] is quite popular in the twitterverse those days