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Shade perception involves altered hormone synthesis and sensitivity. Here, we showed that several shade regulators act as positive and negative modulators of the hypocotyl auxin and/or brassinosteroid-induced elongation.The shade avoidance syndrome (SAS) refers to a set of plant responses initiated after perception by the phytochromes of light enriched in far-red colour reflected from or filtered by neighbouring plants. These varied responses are aimed at anticipating eventual shading from potential competitor vegetation. In Arabidopsis thaliana, the most obvious SAS response at the seedling stage is the increase in hypocotyl elongation. Here, we describe how plant proximity perception rapidly and temporally alters the levels of not only auxins but also active brassinosteroids and gibberellins. At the same time, shade alters the seedling sensitivity to hormones. Plant proximity perception also involves dramatic changes in gene expression that rapidly result in a new balance between positive and negative factors in a network of interacting basic helix–loop–helix proteins, such as HFR1, PAR1, and BIM and BEE factors. Here, it was shown that several of these factors act as auxin- and BR-responsiveness modulators, which ultimately control the intensity or degree of hypocotyl elongation. It was deduced that, as a consequence of the plant proximity-dependent new, dynamic, and local balance between hormone synthesis and sensitivity (mechanistically resulting from a restructured network of SAS regulators), SAS responses are unleashed and hypocotyls elongate. [ABSTRACT FROM PUBLISHER]

PAR1 is an atypical basic-helix-loop-helix (bHLH) protein that negatively regulates the shade avoidance syndrome in Arabidopsis thaliana acting as a transcriptional cofactor. Consistently with this function, PAR1 has to be in the nucleus to display biological activity. Previous structure-function analyses revealed that the N-terminal region of PAR1 drives the protein to the nucleus. However, truncated forms of PAR1 lacking this region still display biological activity, implying that PAR1 has additional mechanisms to localize into the nucleus. In this work, we compared the primary structure of PAR1 and various related and unrelated plant bHLH proteins, which led us to suggest that PAR1 contains a non-canonical nuclear localization signal (NLS) in the N-terminal region. By overexpressing truncated and mutated derivatives of PAR1, we have also investigated the importance of other regions of PAR1, such as the acidic and the extended HLH dimerization domains, for its nuclear localization. We found that, in the absence of the N-terminal region, a functional HLH domain is required for nuclear localization. Our results suggest the existence of a dual mechanism for PAR1 nuclear localization: (1) one mediated by the N-terminal non-consensus NLS and (2) a second one that involves interaction with other proteins via the dimerization domain. [ABSTRACT FROM PUBLISHER]

Basic helix-loop-helix proteins (bHLHs) are found throughout the three eukaryotic kingdoms and constitute one of the largest families of transcription factors. A growing number of bHLH proteins have been functionally characterized in plants. However, some of these have not been previously classified. We present here an updated and comprehensive classification of the bHLHs encoded by the whole sequenced genomes of Arabidopsis (Arabidopsis thaliana), Populus trichocarpa, Oryza sativa, Physcomitrella patens, and five algae species. We define a plant bHLH consensus motif, which allowed the identification of novel highly diverged atypical bHLHs. Using yeast two-hybrid assays, we confirm that (1) a highly diverged bHLH has retained protein interaction activity and (2) the two most conserved positions in the consensus play an essential role in dimerization. Phylogenetic analysis permitted classification of the 638 bHLH genes identified into 32 subfamilies. Evolutionary and functional relationships within subfamilies are supported by intron patterns, predicted DNA-binding motifs, and the architecture of conserved protein motifs. Our analyses reveal the origin and evolutionary diversification of plant bHLHs through differential expansions, domain shuffling, and extensive sequence divergence. At the functional level, this would translate into different subfamilies evolving specific DNA-binding and protein interaction activities as well as differential transcriptional regulatory roles. Our results suggest a role for bHLH proteins in generating plant phenotypic diversity and provide a solid framework for further investigations into the role carried out in the transcriptional regulation of key growth and developmental processes. [ABSTRACT FROM AUTHOR]