Dinoflagellates are unicellular eukaryotes with some of the largest known genomes in their nucleosomeless liquid crystalline chromosomes. Instead of histones, the most abundantly expressed basic proteins are dinoflagellate histone-like proteins (DHLPs). DHLPs have homologies to bacterial histone-like proteins (BHLPs); but they cannot complement BHLP-deficient Escherichia coli mutant. In the present study, amino acid sequences of 48 DHLPs from 15 species of dinoflagellates were further analyzed. Based on their sequence homology, DHLPs were sub-divided into the “early branched” group and the “late branched” group with majority of the extant dinoflagellates. Intriguingly, a novel DNA-binding domain (DBD), which was not found in bacterial HU-homologs, was found conserved in all 48...[ Read more ]

Dinoflagellates are unicellular eukaryotes with some of the largest known genomes in their nucleosomeless liquid crystalline chromosomes. Instead of histones, the most abundantly expressed basic proteins are dinoflagellate histone-like proteins (DHLPs). DHLPs have homologies to bacterial histone-like proteins (BHLPs); but they cannot complement BHLP-deficient Escherichia coli mutant. In the present study, amino acid sequences of 48 DHLPs from 15 species of dinoflagellates were further analyzed. Based on their sequence homology, DHLPs were sub-divided into the “early branched” group and the “late branched” group with majority of the extant dinoflagellates. Intriguingly, a novel DNA-binding domain (DBD), which was not found in bacterial HU-homologs, was found conserved in all 48 DHLPs. This novel DBD evolved from HU’s DNA-binding β-hairpin arm, and only the “late branched” DHLPs harbored fully developed DBD which contributed to their higher DNA aggregation efficiencies. DHLP mutants without their DBD had dramatically decreased DNA aggregation efficiencies. Conversely, the “early branched” DBD mutated to be the more evolved one showed higher DNA aggregation efficiency. Moreover, reduction of basic amino acids (HKb R70T M76E) and change of the conserved large neutral amino acid in DBD (HKb F78A) also led to greatly reduced DNA-aggregation efficiencies. Mutational analyses also suggested that the extra N-terminal tail in some DHLPs collaborated in their DNA-binding. The DHLP of Crypthecodinium cohnii (HCc3) was further investigated for its possible effects on DNA supercoiling. The expression level of HCcs decreased at S phase and peaked at G2/M phase. HCc3 had modulatory effects on the activity of topoisomerase Ⅰ. Immunoprecipitation also revealed HCc3 interacted with topoisomerase Ⅰin Crypthecodinium cohnii. So DHLPs were proposed to participate in supercoiling regulation in dinoflagellates through their modulatory effects on topoisomerase Ⅰ.