The Arabidopsis basic-helix-loop-helix (bHLH) proteins, new partners for phytochrome in light signal transduction

The basic-helix-loop-helix (bHLH) proteins are a superfamily of transcription factors that bind as dimers to specific DNA target sites, and that have been well characterized in non-plant eukaryotes as important regulatory components in diverse biological processes. Based on evidence that the bHLH protein, PIF3, is a direct phytochrome reaction-partner in the photoreceptor's signaling network (Ni et al., 1998), we were interested in investigating if other bHLHs could be involved in phytochrome signaling. To start addressing this question, first we have undertaken a comprehensive computational analysis of the Arabidopsis genome-sequence databases to define the scope and features of the bHLH family. Using a set of criteria derived from a previously defined consensus motif, we initially identified 147 bHLH-protein encoding genes. A later update increased this number to 162 (Bailey et al., 2003), making this one of the largest transcription factor families in Arabidopsis. Phylogenetic analysis of the bHLH-domain sequences permits classification of these genes into 21 subfamilies. PIF3 forms part of the phylogenetic Subfamily 15 with 14 other bHLH proteins (Toledo-Ortiz et al., 2003). The members of At-bHLH Subfamily 15 share extensive sequence similarity to the complete bHLH region of PIF3. Even though sequence homology does not always imply relatedness to the same process, discovery in genetic screens of two more bHLHs members of the Subfamily 15 (PIF4 and HFR1) involved in phytochrome signaling (Huq and Quail, 2000; Frankhauser and Chory, 2000) gave further support to the hypothesis that uncharacterized bHLHs from Subfamily 15 could regulate light signaling. A reverse genetics strategy was used to address this possibility. In this study we targeted in particular PIL1 (Phytochrome Interacting Protein Like 1), to evaluate its role in seedling detiolation and other processes that could be controlled by phytochromes. PIL1 is a gene rapidly down regulated by light. This characteristic made it a good candidate to participate in early events in the signaling cascade. We determined that PIL1 plays a role in the deetiolation responses under Rc as a positive regulator, and that it is also active at later stages of development. PIL1 is not a phytochrome interacting protein (Khanna et al., 2004). However it can heterodimerize with PIF3. At the molecular level, PIL1 could be involved in the induction of a subset of light responsive genes with an acute and early pattern of expression exemplified by one of the members of the At-Pseudo Response Regulator (PRR) protein family, PRR9. (Abstract shortened by UMI.)...