The nuclei of dinoflagellates display a highly derived organisation; chromosomes are permanently condensed and seem to lack histone proteins. A new study in Current Biology links the emergence of these characters to the importation of a novel family of nuclear proteins originating in giant viruses.
Dinoflagellates are a diverse and successful phylum of protists. Many are photosynthetic with a major role in the oceans’ primary production, whilst others have symbiotic, parasitic or predatory lifestyles. Their nuclei are highly unusual. Whereas in all other eukaryotes chromosomes only condense during mitosis, dinoflagellate chromosomes display a permanently condensed, liquid crystalline form. This ‘cholesteric’ structure produces a banded appearance in electron micrographs. Another key dinoflagellate heterodoxy is the absence (or at least undetectability) of histone proteins and the nucleosomal organisation of chromatin. These differences are so radical that dinoflagellates were suggested to represent an intermediate ‘mesokaryotic’ stage between prokarya and eukarya. Molecular phylogenetics has since clarified that they are in fact a sister clade to apicomplexan protists, leaving no doubt that that the dinoflagellate nuclear organisation – the dinokaryon – is derived from standard eukaryotic ancestors. Other atypical features of the dinokaryon include very high DNA content and the replacement of as much as 70% of the base thymine with the rare base 5-hydoxymethyluracil. However, there is some variability in the occurrence of these features. For instance the chromosome banding patterns are not always evident and some dinoflagellate species’ chromosomes can be decondensed at certain stages of their lifecycles.
To investigate the emergence of these dinokaryotic characteristics during the early evolution of the dinoflagellates, Gornik et al. investigated the nuclei of two early-branching members of the lineage. Perkinsus marinus represents the closest known lineage not included within the dinoflagellates proper, whilst Hematodinium sp. branches basally within the clade. In line with their expectations the genome of P. marinus is organised into nucleosomal units, whilst that of Hematodinium sp. is not and appears to be 80 times larger. The P. marinus genome contains sequences for the 4 core histones as well as the linker histone H1, all of which were prominently detectable as protein in extracts from nuclei. Genome sequence is not available for Hematodinium sp., however transcriptomic sequencing revealed the presence of the four core histones as well as a number of variants. Unlike the histone genes of P. marinus the sequences were quite divergent from the highly conserved eukaryotic norm, however the core ‘histone-fold’ regions were relatively well preserved, as were key residues that serve as sites for post-translational modification. Histone genes have been found in other dinoflagellate genomes recently, but histone protein expression had not previously been detected. Gornik et al could identify histone H2A protein in nuclear extracts from Hematotinium sp. However, whereas in P. marinus and other eukaryotes, histone proteins are the dominant species in such extracts, in Hematodinium sp a single 30kDa species dominated.
When this band was extracted and the protein identified by mass spectrometry, it was found to correspond to a novel family of proteins, at least 4 of which were expressed in Hematodinium sp., whilst 13 were found in the transcriptome. This family of proteins only appears to be present in dinoflagellates; no homologues were found in other eukaryotic groups or in prokaryotes. However database searching did reveal homology with a protein of unknown function widely found encoded in the genomes of phycodnaviruses, a family of giant viruses infecting algae. Gornik et al. therefore named these proteins Dinoflagellate/Viral NucleoProteins (DVNPs).
Like histones and many other DNA-binding proteins, DVNPs are highly basic proteins. They are relatively variable in their N-terminal regions, with higher conservation in a core region, which may potentially include a DNA-binding helix-turn-helix motif. Biochemical experiments demonstrated that DVNPs have a high affinity for DNA and are post-translationally modified at various residues by phosphorylation.
The phycodnaviridae are members of the nucleocytoplasmic large DNA viruses (NCLDVs), a monophyletic clade of giant viruses that encode much more of their replication apparatus than is typical of viruses. They are predicted to have emerged more than 2 billion years ago, predating the first dinoflagellates by more than a billion years. As most phycodnaviruses include DVNP orthologues dinoflagellates must have acquired DVNPs from the phycodnaviruses early in their evolution. As yet there is no information on the roles of DVNPs in the phycodnaviridae, but the fact that both taxa have expanded genomes suggests a possible similar function. Do DVNPs allow such efficient DNA packing that the costs of genome expansion are somehow minimised?
The DVNPs are not the first family of putative histone-replacement proteins discovered in dinoflagellates. Later-branching taxa express ‘histone-like proteins’ (HLPs), probably related to the bacterial DNA-binding protein HU, and shown to be able to bend DNA in vitro. HLPs are not found in Hematodinium sp. or other early-branching dinoflagellates, whereas DVNPs are found in combination with HLPs in later-branching taxa. DVNPs therefore seem to be associated with the core dinokaryotic characteristics of permanently condensed chromosomes and expanded genome size, whilst the presence of HLPs correlates with other characters such as the chromosome banding patterns observed in later-branching taxa.
The observation that dinoflagellates do in fact encode and express divergent histones at low levels raises the question of what their roles could be if they are not primarily responsible for the bulk packing of DNA? Linked to this is the broad question of how DVNPs and HLPs act to condense dinoflagellate chromosomes. Considering the vast quantity of research attempting to understand the biology of eukaryotic chromosomes, it is rather daunting to find a whole new way of doing things; how do transcription and replication mechanisms work in the context of permanently condensed chromosomes? How does this link in with genome expansion? I don’t know how much dinoflagellate genomic data is available, but I imagine that a finished genome sequence would be of great use. Perhaps though, I’d prefer instead to prioritise biochemical and structural studies of these various proteins actions on DNA.
Gornik, S., Ford, K., Mulhern, T., Bacic, A., McFadden, G., & Waller, R. (2012). Loss of Nucleosomal DNA Condensation Coincides with Appearance of a Novel Nuclear Protein in Dinoflagellates Current Biology DOI: 10.1016/j.cub.2012.10.036