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).


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