Dinoflagellates are ecologically important, unicellular eukaryotes in aquatic environments. They have unusual, permanently condensed chromosomes and immense nuclear genome sizes. Recent advances in dinoflagellate biology have revealed many novel genomic features. The first draft genome of the dinoflagellate, Symbiodinium minutum, displays unique and derived characteristics (http://marinegenomics.oist.jp/genomes/gallery). (1) The genome comprises approximately 42,000 protein-coding genes, including highly duplicated genes for regulator-of-chromosome-condensation proteins. One-third of these have eukaryotic orthologs, whereas the others have similarities to those of bacteria. (2) Symbiodinium genes are enriched in spliceosomal introns (average 18.6 introns/gene), in which donor and accepter splice sites are unique. (3) All spliceosomal snRNA genes, spliced-leader genes, and 5S rRNA genes are clustered in the genome. (4) The Symbiodinium genome displays unidirectionally aligned genes throughout the genome, forming a cluster-like gene arrangement. Here I briefly introduce recent advances in dinoflagellate genomics, paying special attention to the genome structures of gene-rich regions.
Most eukaryotes have motile cilia/flagella as cell organelles for swimming, locomotion, or generating extracellular fluid flow. Recent studies have revealed that dysfunctions in ciliary/flagellar motility engender human disease. Most motile cilia/flagella possess the inner structure called the axoneme with “9 + 2” pattern, in which the nine doublet microtubules surround two central singlet microtubules. This structural pattern is evolutionally conserved. The axoneme comprises many structural components aligned on the microtubules, including axonemal dyneins, radial spokes, and projections on the central pair microtubules. Ciliary/flagellar movements are generated by dynein-driven microtubule sliding, and are controlled by second messengers such as Ca2+ and cAMP. However, molecular mechanisms of ciliary/flagellar movements in response to Ca2+ and cAMP, and the individual roles of the axonemal components in the mechanisms remain unclear. Furthermore, mechanisms by which the energy is supplied for ciliary/flagellar movement are not well defined. Paramecium has long been used as a model organism for studying ciliary motility, because of its valuable experimental systems. For example, cell excitement can be analyzed elecrophysiologically, and cilia on demembranated cell models and cortical sheets can be reactivated in vitro. Furthermore, protocols for RNAi depletion of specific genes, as well as the genome and the ciliary proteome databases, became available recently. This review describes recent studies on molecular mechanisms of ciliary movements in Paramecium, highlighting intraciliary energy-supply systems and regulatory systems by Ca2+ and cAMP.
Living cells are deeply divided into two enormously divergent levels of complexity: prokaryotic and eukaryotic. Eukaryotes are thought to have developed from prokaryotic predecessors; however the large differences in their cellular structures results in equally large questions of how the process might have occurred. In 2012, in the deep-sea off the coast of Japan, we discovered a unique microorganism appearing to have cellular features intermediate between prokaryotes and eukaryotes. The organism, the Myojin parakaryote (tentatively named by Yamaguchi et al., 2012), was two orders of magnitude larger than a typical bacterium and had a large “nucleoid”, consisting of naked DNA fibers, surrounded by a single layered “nucleoid membrane”, and bacteria-like “endosymbionts”, but it lacked mitochondria. This organism exemplifies a potential evolutionary path between prokaryotes and eukaryotes, and strongly supports the endosymbiotic theory for the origin of mitochondria and the karyogenetic hypothesis for the origin of the nucleus. In this review, we describe how the Myojin parakaryote was discovered, the features of this organism, the significance of the discovery, and perspectives on future research.
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