Insights into Nitrogen-Associated Protein 50 (NAP50) as a Tyrosyl–DNA Phosphodiesterase in Dinoflagellates

Nitrogen-associated protein 50 (NAP50) is an abundant plastid protein with an unknown function identified in Alexandrium affine (Dinophyceae). No progress has been made in discovering the function of NAP50 since its first characterization in 2009. The present study is a continuation of work on the predicted function of NAP50. The results show that the NAP50 gene lacks introns but contains abundant base substitutions, consistent with the characteristics of dinoflagellate nuclear genes. The NAP50 protein is found to be widely expressed in dinoflagellate lineages through bioinformatics analysis and Western blotting, suggesting that NAP50 is not exclusive to Alexandrium, which differs from previous understandings. Phylogenetic analysis reveals that NAP50 belongs to the tyrosyl–DNA phosphodiesterase (TDP) family; however, it is structurally distinct from the TDP2 that is present in some dinoflagellate species. The three-dimensional structure and biological functions of NAP50 are predicted using deep learning algorithms. Based on evolutionary relationships and functional predictions, NAP50 may play a role in repairing plastid DNA damage and potentially contribute to the transcription of plastid genes in dinoflagellates.