Genome-wide identification, transcriptional analysis, and acetylated histone site recognition of the Bromodomain gene family in Pyropia yezoensis

Abstract

The bromodomain (BRD) is a protein domain that recognizes acetylated lysine residues and plays a pivotal role in chromatin remodeling and the recruitment of transcription factors, thereby regulating gene transcription. Although extensively studied in animals and plants, the presence and function of BRD genes in red algae remain unexplored. This study identified 10 BRD family genes in red seaweed, Pyropia yezoensis, all of which encode proteins with conserved bromodomains. Six of these proteins (PyGTE9, PyNPX, PyGTE7, PyGCN5, PyBRAT, and PyBRD-WD40) exhibited a highly conserved domain organization similar to that of plant BRDs. Additionally, a unique BRD type, Tudor, was found exclusively in red algae and possibly had dual histone acetylation and methylation affinities. Regarding evolutionary dynamics, the number of BRD family members in P. yezoensis was highly conserved in Rhodophyta, albeit exhibited a distant phylogenetic relationship with Arabidopsis thaliana. Interestingly, some red-algae-specific BRD genes were discovered. Collinearity analysis showed that all BRD genes were syntenic in P. yezoensis and P. haitanensis. Pull-down assays with acetylated histone peptides revealed that the BRD of PyGTE9 has a strong binding affinity to H3K18ac, H4K5ac, H4K8ac, and H4K16ac. Finally, transcriptional profile analysis further revealed that these BRD genes exhibited differential expression under wound stress and dehydration stress across two generations of P. yezoensis. In summary, our findings provide an understanding of the evolutionary, structural, and transcriptional dynamics under abiotic stresses of the P. yezoensis BRD family members and further clarify the histone recognition attributes of PyGTE9. This study provides valuable insights for future research into the function of the P. yezoensis BRD family genes.