The green site of TRANSFAC: Gene regulation controlled by MYB related factors in plants


	The green site of TRANSFAC:


	Gene regulation controlled by MYB related factors in plants


	Robert Geffers (rge@biobase.de), Edgar Wingender (ewi@biobase.de) Biobase Biological Databases GmbH, Mascheroder Weg 1b, D-38124 Braunschweig


	Introduction

Recently the TRANSFAC database was supplemented with MYB related factors from plants. Originally MYB factors in vertebrates are proto-oncogenes. First identified as a homologous (figure 1) of the transforming gene in avian myeloblastosis, mammalian MYBs are mainly involved in controlling cellular proliferation. In contrast MYB related factors in plants acts in regulation of many different, mainly plant specific processes. Today the best studied MYB regulated process is the coordinated gene transcription of the phenylpropanoid metabolism (figure 2). Other processes followed after the characterization of an increasing number of MYB factors in plants (i.e. figure 3-5). Therefore in respect of understanding regulation of plant specific processes, the knowledge of MYB related factors is essential. TRANSFAC now contains most of these factors and their target genes (central box).


	Structural features


	Phenylpropanoid metabolism

Figure 1: Conserved AA features of Myb factors in plants.
The DNA binding domain consists of three 50 aa repeats in animals (R1-R3), whereas in plants only two repeats (in some cases only one) were detected. These repeats show most striking homology to the animal R2 and R3. One repeat consists of 3 -helices (bars). The third helix (brown bar) of the R2 and R3 repeat is in contact to the major groove of the DNA molecule. Within these repeats a characteristic feature is common to all MYB factors: the tryptophan cluster. Three tryptophan residues are spaced by 18-21 aa which are very conserved among all MYB factors (red boxes).

Figure 2: Schematic presentation of the most important steps in the synthesis of the pigments anthocyanin and phlobaphene. MYB factors of different species interact with promoter elements of several key genes (blue letters). The recognition sites of these factors within the promoters are very similar. C1 activates his target genes only in presence of cell specific MYC factors (bHLH transcription factor).

Abbreviations: PAL Phenylalanine lyase, CHS Chalcone synthase, CHI Chalcone isomerase, F3H Flavanone-3-hydroxylase, DFR Dihydroflavonol reductase, ANS Anthocyanidinsynthase, UF3GT UDP-Glycosyl-transferase


	Regulation of MYB binding activity

Ø	Cellular redox potential	P as c-Myb requires a reduced REDOX state to bind DNA; may be a very conserved C53 (C130 in c-Myb) serves as molecular sensor.
Ø	Phosphorylation	Dephosphorylation of MYB340 switches the DNA-binding affinity from low to high; phosphorylation of CCA1 stimulates its binding activity.
Ø	Interaction	Interaction with several MYC factors (i.e. C1 and B; GL1 and TTG)
Ø	Competition interaction	Myb factor with similiar DNA recognition compete for the same binding sequence but activate in different modi (MYB305/MYB340, C1/CI)


	Circadian regulation



	Figure 3: The transcription of the Lhcb (light harvesting complex b), a protein involved in photosynthesis is regulated by the MYB factor CCA1 in a light dependent manner. In turn the activating potential of this factor is also regulated by phosphorylation by CK2. Light perception may be mediated by Phytochrom A (dashed arrows). The photoperiodic rhythm can adjust by the "internal clock", feedback loop or light and transduce this information to other effector genes like CCR2 (indirectly; dashed arrow). LHY is supposed to be regulated and regulate their target genes in a very similiar manner and shows strong homology to CCA1. Mutants of LHY show photoperiodic independent later flowering and longer hypocotyls.


	Hormonal response


	Trichome and root hair formation

Figure 4: Examples how MYB factors can be regulated or activated by different plant specific hormones. Under long day conditions the transcription rate of GAMYB increases mediated by an elevating level of gibberrellic acid (GA) . The target gene could be a LEAFY homolog with potential binding sites of MYB factors within the promoter. A distinct GAMYB activates germination specific genes.
Another plant hormone, absisic acid (ABA), initiates stress responses. Increasing levels of ATMYB2 induced by ABA regulate transcription of some stress genes. rd22 activation depends on ATMYB2 in combination with a MYC factor similar to C1 and R/B in the phenylpropanoid pathway. In this context, ATMYB2 is able to bind the MYB site within the UF3GT promoter. Furthermore C1 is also regulated by ABA.


	Figure 5: In A. thaliana two MYB factors are involved in the trichome and root hair formation. GL1 and CPC controlls thereby the homeo


	domain factor GL2 in a distinct manner. GL1 influences GL2 positively, leading to the formation trichomes on leaves. May be the activation of the target gene(s) of GL1 depends on the presence of TTG. In contrast, ectopically expression of the root specific CPC blocks GL2 expression and abolishes trichome formation (upper picture).

In turn GL2 blocks the root hair formation. Ectopically expression of CPC leads to multi hair formation in comparison to wild type (lower picture B/C). Mutant CPC forms no root hairs (picture A). As it was mentioned for GL1 CPC also could act together with TTG in activating its target genes.
In context to trichome formation a few other MYB factors are important. MIXTA and MYB1 are involved in cell shape formation, which means a early termination of the trichome development.


	Perspectives and TRANSFAC

The presented data is only a small example of the information implemented in the TRANSFAC database so far (Fig 6). Nevertheless, there is much work to do covering all the published data of plant specific gene regulation. In the last 3 months the factor entries are nearly doubled followed by information on their regulating genes. To maintain our leading position in providing information of gene regulation we are grateful to set up a cooperation with TU Braunschweig supporting us with latest information in the area of plant specific gene regulation.

Table	TRANSFAC	TRANSFAC / Plant
SITE	8698	166
Gene	1371	115
Factor	3127	469
Matrix	380	31
CELLS	1035	-
REFERENCE	11108	-
SPECIES	232	67


	Figure 6: Contents of TRANSFAC