The phytochrome-interacting factor genes PIF1 and PIF4 are functionally diversified due to divergence of promoters and proteins

Species-specific PHYTOCHROME-INTERACTING FACTOR utilization in the plant morphogenetic response to environmental stimuli

PHYTOCHROME-INTERACTING FACTORs (PIFs) regulate growth-related gene expression in response to environmental conditions. Among their diverse functions in regulating signal responses, PIFs play an important role in thermomorphogenesis (the response to increased ambient temperature) and in the shade avoidance response. While numerous studies have examined the varied roles of PIFs in Arabidopsis (Arabidopsis thaliana), their roles in crop plants remain poorly investigated. This study delves into the conservation of PIFs activity among species by examining their functions in tomato (Solanum lycopersicum) and comparing them to known PIF functions in Arabidopsis using single and higher-order mutants of tomato PIF genes (SlPIFs). We demonstrate that, in contrast to Arabidopsis, PIFs are not required for thermomorphogenesis-induced stem elongation in tomato. In addition, whereas Arabidopsis PIF8 has a minor effect on plant growth, tomato SlPIF8a plays a key role in the low red/far-red (R/FR) response. In contrast, SlPIF4 and SlPIF7s play minor roles in this process. We also investigated the tissue-specific low R/FR response in tomato seedlings and demonstrate that the aboveground organs exhibit a conserved response to low R/FR, which is regulated by SlPIFs. Our findings provide insights into PIF-mediated responses in crop plants, which may guide future breeding strategies to enhance yield under high planting densities.

Specific binding between Arabidopsis thaliana phytochrome-interacting factor 3 (AtPIF3) bHLH and G-box originated prior to embryophyte emergence

The basic helix-loop-helix (bHLH) domain via critical amino acid residues on basic region binding to E-box (5'-CANNTG-3') is known in embryophyte. However, the dictated E-box types selection by bHLH dimers and the significant impact of these critical amino acid residues along embryophyte evolution remain unclear. The Arabidopsis thaliana PIF3-bHLH (AtPIF3-bHLH) recombinant protein and a series of AtPIF3-bHLH mutants were synthesized and analyzed. The reduced DNA binding ability and affinity of AtPIF3-bHLH point-mutation proteins, observed via fluorescence-based electrophoretic mobility shift assay (fEMSA) and isothermal titration calorimetry (ITC), suggest the critical role of these DNA-recognition sites in maintaining the AtPIF3-bHLH-DNA interaction. The purifying selection signals and the DNA-recognition-site conservation at the species level suggest the invariant roles of these sites throughout embryophyte evolution. The G-box outcompeted other types of E-box for binding in our competitive fEMSAs. The dynamic hydrogen bond formed between AtPIF3-bHLH and the G-box core indicates flexible identification of the core region. These features highlight a fast fixation of the bHLH-G-box recognition mechanism through embryophyte evolution and serve as a blueprint for studying DNA recognition determinants of other TF families.

Evolution and Domestication of a Novel Biosynthetic Gene Cluster Contributing to the Flavonoid Metabolism and High-Altitude Adaptability of Plants in the Fagopyrum Genus

The diversity of secondary metabolites is an important means for plants to cope with the complex and ever-changing terrestrial environment. Plant biosynthetic gene clusters (BGCs) are crucial for the biosynthesis of secondary metabolites. The domestication and evolution of BGCs and how they affect plant secondary metabolites biosynthesis and environmental adaptation are still not fully understood. Buckwheat exhibits strong resistance and abundant secondary metabolites, especially flavonoids, allowing it to thrive in harsh environments. A non-canonical BGC named UFGT3 cluster is identified, which comprises a phosphorylase kinase (PAK), two transcription factors (MADS1/2), and a glycosyltransferase (UFGT3), forming a complete molecular regulatory module involved in flavonoid biosynthesis. This cluster is selected during Tartary buckwheat domestication and is widely present in species of the Fagopyrum genus. In wild relatives of cultivated buckwheat, a gene encoding anthocyanin glycosyltransferase (AGT), which glycosylates pelargonidin into pelargonidin-3-O-glucoside, is found inserted into this cluster. The pelargonidin-3-O-glucoside can help plants resist UV stress, endowing wild relatives with stronger high-altitude adaptability. This study provides a new research paradigm for the evolutionary dynamics of plant BGCs, and offers new perspectives for exploring the mechanism of plant ecological adaptability driven by environmental stress through the synthesis of secondary metabolites.