A shade-responsive microProtein in the Arabidopsis ATHB2 gene regulates elongation growth and root development

The ability of plants to thrive under suboptimal light conditions, such as shade, is crucial for their overall survival and reproductive success. Here, we show that Arabidopsis seedlings produce a large number of alternative transcripts when exposed to shade. Notably, one of the identified transcript candidates, which was upregulated in shade conditions, was found to be an alternative transcript of the ATHB2 gene. ATHB2 belongs to the HD-ZIPII class of transcription factors and is a well-established regulator of the shade avoidance response. The function of the alternative transcript and the small leucine zipper protein encoded by it, ATHB2miP, was investigated. We found that ATHB2miP is primarily expressed in the shoot meristem and interacts with full-length ATHB2 protein to inhibit its activity through a negative feedback mechanism. Deletion of the genomic region encoding the leucine zipper domain of the ATHB2 gene using CRISPR, resulted in plants exhibiting altered shade avoidance responses and root development. We show that the leucine zipper domain is required for dimerising and localising to nuclear photobodies. There is a significant overlap in deregulated genes between plants ectopically expressing ATHB2miP and athb2 mutant plants. The analysis of gene ontology and clustering revealed that the most affected processes are auxin synthesis and signaling, root development, and iron homeostasis. Shade growth experiments at different iron concentrations revealed a role for ATHB2 in regulating iron uptake and showed that iron availability affects shade growth in an ATHB2-dependent manner. This study identifies ATHB2miP as a novel regulator of shade avoidance responses in Arabidopsis, highlighting the intricate transcriptional regulation underlying these processes.