Histone-like proteins of the dinoflagellate Crypthecodinium cohnii have homologies to bacterial DNA-binding proteins

Abstract

The dinoflagellates have very large genomes encoded in permanently condensed and histoneless chromosomes. Sequence alignment identified significant similarity between the dinoflagellate chromosomal histone-like proteins of Crypthecodinium cohnii (HCCs) and the bacterial DNA-binding and the eukaryotic histone H1 proteins. Phylogenetic analysis also supports the origin of the HCCs from histone-like proteins of bacteria.

FIG. 1.

Alignment of HCCs with HUs, histone-like proteins, and histone H1. (A) Multiple alignments of HCCs and selective bacterial HUs: HCC1 (A56581), HCC2 (B56581), HCC3 (AY128510), and HCC4 (AY128511); HU-Pa (Pseudomonas aeruginosa, JC4061); HU-Dr (Deinococcus radiodurans, Q9RZ89); HU-St (Salmonella enterica serovar Typhimurium, S01732); HU-Hi (Haemophilus influenzae, P43722); and HU-Sp (Streptococcus pneumoniae, AAK75224). (B) Multiple alignments of dinoflagellate and bacterial histone-like proteins: HLP (L. polyedrum, AF482694), HAF (A. fundyense, AAD20317), BpH2 (B. pertussis, AAB40156), and XHLP (X. fastidiosa 9a5c, AAF84745). (C) Multiple alignments of HCCs and selective eukaryotic histone H1 proteins: H1-Ce (Caenorhabditis elegans, NP_510410), H1-Gg (Gallus gallus, P09987), H1′-Hs (Homo sapiens, XP_009973), and H1-Mm (Mus musculus, AAA37814). Asterisks indicate positions which have a single, fully conserved residue; colons indicate that one of the “strong” groups in parentheses is fully conserved (STA/NEQK/NHQK/NDEQ/QHRK/MILV/MILF/HY/FYW); periods indicate that one of the “weaker” groups in parentheses is fully conserved (CSA/ATV/SAG/STNK/STPA/SGND/SNDEQK/NDEQHK/NEQHRK/FVLIM/HFY).

FIG. 2.

A phylogenetic tree (UPGMA) inferred from the multiple alignments of amino acid sequences of histone-like proteins from dinoflagellate HCCs (a), bacterial histone-like protein family (b), and bacterial DNA-binding HU proteins (c) was constructed with PHYLIP version 3.5. The numbers at the nodes represent the bootstrap percentages by creation of 500 replicated data sets with SEQBOOT. The accession number for each protein sequence is as follows: HCC1 (C. cohnii), A56581; HCC2 (C. cohnii), B56581; BpH2 (B. pertussis), AAB40156; XHLP (X. fastidiosa), AAF84745; HU (Salmonella enterica serovar Typhimurium), S01732; HU (Streptococcus pneumoniae), AAK75224; HU (Haemophilus influenzae), P43722; HU (Pseudomonas aeruginosa), JC4061; HU (Deinococcus radiodurans), Q9RZ89.