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Plant Signal Behav. 2010 February; 5(2): 200–201.
PMCID: PMC2884135

Shedding light on the role of AT-hook/PPC domain protein in Arabidopsis thaliana


Flower reproductive development is a complex process involving well-coordinated control of transcriptional regulation cascades. AGAMOUS (AG) plays an instrumental role in the specification and differentiation of reproductive organs in Arabidopsis thaliana. We recently characterized a downstream target gene of AG, GIANT KILLER (GIK), which encodes for an AT-hook/plants and prokaryotes conserved (PPC) domain protein. We found that overexpression of GIK leads to severe reproductive defects and downregulation of genes involved in patterning and differentiation of reproductive floral organs. We showed that GIK is a matrix protein, and GIK-mediated gene regulation requires binding of GIK to matrix associated region (MAR) of the target genes. We further showed that GIK-mediated negative regulation of one of the target genes, ETTIN (ETT), is associated with changes of chromatin histone modification at ETT promoter, suggesting that GIK acts as a gene expression modulator through chromatin organization.

Key words: Arabidopsis, GIK, AT-hook, PPC domain, nuclear organization, fine-tuning

AGAMOUS (AG), a class C gene in the famous ABC model of flower development,1 has long been regarded as a master regulator of reproductive development in Arabidopsis thaliana.2,3 It is a long-standing mystery as to how AG regulates its multiple downstream targets and how it ensures the entire transcriptional process is well-coordinated. We recently identified and characterized a downstream target of AG, GIANT KILLER (GIK),4 which has the ability to modulate expression of several transcriptional regulators involved in reproductive development. GIK belongs to an AT-hook/PPC domain-containing protein family in Arabidopsis. There are more than 20 GIK-like genes present in the Arabidopsis genome, which share substantial sequence homology.59

In our studies, we showed that GIK modulated the expression of several key regulators of reproductive differentiation and patterning like ETTIN (ETT), CRABS CLAW (CRC), JAGGED (JAG) and KNUCKLES (KNU). We demonstrated that overexpression of GIK caused wide-ranging defects in reproductive development and also resulted in downregulation of ETT, CRC, JAG and KNU expression. GIK-mediated gene regulation requires the presence of matrix associated region (MAR) in the genomic sequences of the target genes, which serves as a binding site for the AT-hook DNA binding protein.

We further demonstrated that GIK-mediated negative regulation of the target gene was closely linked with histone modification, in particular, H3K9 dimethylation, as highlighted in the rapid and dynamic change of histone mark on ETT promoter upon GIK activation. Nevertheless, it still remains unclear on how overexpression of GIK could lead to a change in the chromatin state. Since GIK lacks any known domain that could catalyze a direct deposition of repressive histone mark, it is speculated that it may act through other protein factors. There are two possible ways that GIK could be involved in the modulation of gene expression. In the first model, GIK can actively recruit protein complexes containing chromatin-modifying enzymes to carry out deposition of silencing mark on histone tails (Fig. 1A). Hence, overexpression of GIK would lead to an overwhelmed accumulation of the enzymes at the site and a decrease in target gene expression. It would be tempting to know if the PPC domain of GIK has any function on protein-protein interaction that would mediate the recruitment of these protein factors. The second model predicts that an elevated level of GIK may result in its excessive tethering of MARs of the target genomic sequence and this would bring active transcribing genes in closer proximity to the nuclear matrix, causing a trans-silencing of the target genes (Fig. 1B). Interestingly, there are reports that introduction of MARs into transgenes could increase their expression in plants.10,11 It still remains unknown whether concomitant increase of AT-hook binding proteins in these contexts would diminish the enhanced expression of the transgenes caused by MARs.

Figure 1
The proposed models of GIK-mediated negative regulation of target genes. (A) Direct recruitment of chromatin modifying enzymes. The direct interaction between the PPC domain of GIK and the nuclear matrix depicted in the schematic diagram is hypothetical; ...

The interaction between GIK AT-hook motif and MARs of the ETT promoter is relatively weak and transient. The AT-hook motif, as suggested by a number of findings, 1214 acts through binding of DNA minor groove and could cause changes in chromatin architecture. As an expansion of the second model, the binding of GIK AT-hook motif towards the MAR might be adopting a ‘search-capture-release’ mode, and is possibly involved in a constant ‘tug-of-war’ with the positive regulators of ETT to balance and fine-tune the expression of ETT. This also might explain why the expression of GIK has to be maintained at an appropriate level.



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