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Dinoflagellates possess plastids that are diverse in both pigmentation and evolutionary background. One of the plastid types found in dinoflagellates is pigmented with chlorophylls a and b (Chl a + b ) and originated from the endosymbionts belonging to a small group of green algae, Pedinophyceae. The Chl a + b -containing plastids have been found in three distantly related dinoflagellates Lepidodinium spp., strain MGD, and strain TGD, and were proposed to be derived from separate partnerships between a dinoflagellate (host) and a pedinophycean green alga (endosymbiont). Prior to this study, a plastid genome sequence was only available for L. chlorophorum , which was reported to bear the features that were not found in that of the pedinophycean green alga Pedinomonas minor , a putative close relative of the endosymbiont that gave rise to the current Chl a + b -containing plastid. In this study, we sequenced the plastid genomes of strains MGD and TGD to compare with those of L. chlorophorum as well as pedinophycean green algae. The mapping of the RNA-seq reads on the corresponding plastid genome identified RNA editing on plastid gene transcripts in the three dinoflagellates. Further, the comparative plastid genomics revealed that the plastid genomes of the three dinoflagellates achieved several features, which are not found in or much less obvious than the pedinophycean plastid genomes determined to date, in parallel.

Cryptophyte and chlorarachniophyte algae are transitional forms in the widespread secondary endosymbiotic acquisition of photosynthesis by engulfment of eukaryotic algae. Unlike most secondary plastid-bearing algae, miniaturized versions of the endosymbiont nuclei (nucleomorphs) persist in cryptophytes and chlorarachniophytes. To determine why, and to address other fundamental questions about eukaryote–eukaryote endosymbiosis, we sequenced the nuclear genomes of the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans . Both genomes have >21,000 protein genes and are intron rich, and B. natans exhibits unprecedented alternative splicing for a single-celled organism. Phylogenomic analyses and subcellular targeting predictions reveal extensive genetic and biochemical mosaicism, with both host- and endosymbiont-derived genes servicing the mitochondrion, the host cell cytosol, the plastid and the remnant endosymbiont cytosol of both algae. Mitochondrion-to-nucleus gene transfer still occurs in both organisms but plastid-to-nucleus and nucleomorph-to-nucleus transfers do not, which explains why a small residue of essential genes remains locked in each nucleomorph. Sequencing the nuclear genomes of Guillardia theta and Bigelowiella natans , transitional forms in the endosymbiotic acquisition of photosynthesis by engulfment of certain eukaryotic algae, reveals unprecedented alternative splicing for a single-celled organism ( B. natans ) and extensive genetic and biochemical mosaicism, shedding light on why nucleomorphs persist in these species but not other algae. Evolutionarily complex algal genomes revealed This paper presents the sequences of the nuclear genomes of two eukaryotic microbes of remarkable genetic and cellular complexity, Guillardia and Bigelowiella . These algae are transitional forms in the endosymbiotic acquisition of photosynthesis by engulfment of eukaryotic algae, and possess four genomes: mitochondrial and plastid (chloroplast) genomes, a nuclear genome of host origin and a miniaturized 'nucleomorph' genome of endosymbiotic origin. Analyses reveal unprecedented alternative splicing for a single-celled organism, and extensive genetic and biochemical mosaicism. Whereas the mitochondrion-to-nucleus gene transfer continues in both organisms, plastid-to-nucleus and nucleomorph-to-nucleus transfers have ceased, explaining nucleomorph persistence.

The morphology of two marine woloszynskioid dinoflagellates from the Japanese coast was examined by light, scanning and transmission electron microscopy, and phylogenetic positions were inferred on the basis of partial nuclear-encoded large-subunit ribosomal (r)DNA (D1-D3) sequences. Both species had a single elongate apical vesicle (EAV) on the anterior end, a diagnostic feature of the Suessiaceae, and were identified as Biecheleriopsis adriatica and an undescribed species of Biecheleria. Cells of the undescribed Biecheleria were spherical to ellipsoidal with parietal chloroplasts, conspicuous pyrenoids, an eyespot, and a nucleus located anteriorly. Transmission electron microscope observations revealed penetrations of the thylakoid into the pyrenoid matrix and an eyespot composed of a stack of cisternae containing several brick-like materials (type E). This species had a total of nine to 10 latitudinal series of amphiesmal vesicles (AVs), including three to fo ur epiconal, three cingular, and three hypoconal series. Nineteen small globular knobs were present on the EAV. This species was distinguished from other marine woloszynskioids by cell size, position of nucleus, and the number of AV series and EAV knobs, i.e. previously reported Biecheleria have more than 25 knobs. We describe a new marine woloszynskioid dinoflagellate Biecheleria brevisulcata sp. nov. The Japanese strains of Bps. adriatica had 11-12 series of AVs in total, including four to five epiconal, three cingular, and four hypoconal series, and there were 32 knobs on the EAV. The features of these strains basically coincided with those of the original description of Bps. adriatica, but differed in the larger number of EAV knobs. Molecular phylogeny also indicated their affinity to the Suessiaceae. Strains of B. brevisulcata formed a clade related to B. baltica and B. cincta. The two genera, Biecheleria and Biecheleriopsis, have a strong morphological resemblance to one another, and they were distinguished only by rDNA sequences and the presence of a fibrous flagellar root (nuclear connective). This study also showed a morphological difference between the two genera; vesicles of the third row of cingular vesicles were larger and the lower cingular margin had a zigzag line in Biecheleria, whereas they were smaller and formed a straight line in Biecheleriopsis, especially on the dorsal side.

Nucleomorphs are relic endosymbiont nuclei so far found only in two algal groups, cryptophytes and chlorarachniophytes, which have been studied to model the evolutionary process of integrating an endosymbiont alga into a host-governed plastid (organellogenesis). However, past studies suggest that DNA transfer from the endosymbiont to host nuclei had already ceased in both cryptophytes and chlorarachniophytes, implying that the organellogenesis at the genetic level has been completed in the two systems. Moreover, we have yet to pinpoint the closest free-living relative of the endosymbiotic alga engulfed by the ancestral chlorarachniophyte or cryptophyte, making it difficult to infer how organellogenesis altered the endosymbiont genome. To counter the above issues, we need novel nucleomorph-bearing algae, in which endosymbiont-to-host DNA transfer is on-going and for which endosymbiont/plastid origins can be inferred at a fine taxonomic scale. Here, we report two previously undescribed dinoflagellates, strains MGD and TGD, with green algal endosymbionts enclosing plastids as well as relic nuclei (nucleomorphs). We provide evidence for the presence of DNA in the two nucleomorphs and the transfer of endosymbiont genes to the host (dinoflagellate) genomes. Furthermore, DNA transfer between the host and endosymbiont nuclei was found to be in progress in both the MGD and TGD systems. Phylogenetic analyses successfully resolved the origins of the endosymbionts at the genus level. With the combined evidence, we conclude that the host–endosymbiont integration in MGD/TGD is less advanced than that in cryptophytes/chrorarachniophytes, and propose the two dinoflagellates as models for elucidating organellogenesis.

NOP56, a core nucleolar component involved in small nucleolar ribonucleoprotein assembly, has been genetically implicated in spinocerebellar ataxia type 36. However, the role of NOP56 in mammalian neurodevelopment and disease remains poorly defined. We investigated NOP56 pathobiology using both in vitro induced pluripotent stem cell-derived neurons and in vivo NOP56 knockout mouse models. NOP56 expression significantly decreased both in the spinocerebellar ataxia type 36 patients induced pluripotent cells and induced pluripotent cell-derived neurons, which suggests the possibility that the NOP56 loss of function is involved in the spinocerebellar ataxia type 36 phenotype. Therefore, we generated and validated the NOP56 knockout mouse phenotype. Homozygous NOP56 deletion resulted in total embryonic lethality; no NOP56 progeny was viable at birth. Heterozygous knockouts showed clasping at 8 months of age and had a larger body size with aging, although there was no significant difference in survival between heterozygous and wild type. Heterozygous knockout mice showed deterioration in rotarod performance and a decrease in exploration behavior. Immunohistochemical analysis of the heterozygous knockouts revealed widespread, significant central nervous system abnormalities, particularly cerebellar degeneration, accompanied by motor cortex and spinal cord disturbances. Widespread ubiquitin-positive inclusions were detected in the cerebellum, motor cortex, and anterior spinal cord of the heterozygous knockout mice at the 12-month age, and it was positive from the 6-month age in the cerebellum. Colocalizations of TDP-43 and ubiquitin were observed in the motor cortex, spinal cord, and cerebellum. Along with findings from previous reports showing early downregulation of NOP56 in SOD1 G93A transgenic mice, this finding indicates that NOP56 might be involved in a wide range of motor neuron diseases. The pathological characteristics of the NOP56 heterozygous knockouts are like those of a patient with spinocerebellar ataxia type 36. Results reveal that NOP56 is indispensable for mammalian embryogenesis and central nervous system maintenance, and that its reduction contributes to molecular pathology in spinocerebellar ataxia type 36. These findings uncover a convergent neurodegenerative mechanism and identify NOP56 as a potential therapeutic target.Clinical trial registrationThis study was registered with the Japan Clinical Trials Registry (http//umin.ac.jp/ctr/index/htm), under the number UMIN000047097.

Cryptophyte and chlorarachniophyte algae are transitional forms in the widespread secondary endosymbiotic acquisition of photosynthesis by engulfment of eukaryotic algae. Unlike most secondary plastid-bearing algae, miniaturized versions of the endosymbiont nuclei (nucleomorphs) persist in cryptophytes and chlorarachniophytes. To determine why, and to address other fundamental questions about eukaryote eukaryote endosymbiosis, we sequenced the nuclear genomes of the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans. Both genomes have 21,000 protein genes and are intron rich, and B. natans exhibits unprecedented alternative splicing for a single-celled organism. Phylogenomic analyses and subcellular targeting predictions reveal extensive genetic and biochemical mosaicism, with both host- and endosymbiont-derived genes servicing the mitochondrion, the host cell cytosol, the plastid and the remnant endosymbiont cytosol of both algae. Mitochondrion-to-nucleus gene transfer still occurs in both organisms but plastid-to-nucleus and nucleomorph-to-nucleus transfers do not, which explains why a small residue of essential genes remains locked in each nucleomorph.

Nucleomorphs are relic endosymbiont nuclei so far found only in two algal groups, cryptophytes and chlorarachniophytes, which have been studied to model the evolutionary process integrating an endosymbiont alga into be a host-governed plastid (organellogenesis). Nevertheless, past studies suggested that DNA transfer from the endosymbiont to host nuclei had already ceased in both cryptophytes and chlorarachniophytes, implying that the organellogenesis at the genetic level has been completed in the two systems. Moreover, we have yet to pinpoint the closest free-living relative of the endosymbiotic alga engulfed by the ancestral chlorarachniophyte or cryptophyte, making difficult to infer how organellogenesis altered the endosymbiont genome. To counter the above issues, we need novel nucleomorph-bearing algae, in which from-endosymbiont-to-host DNA transfer is on-going and of which endosymbiont/plastid origins can be inferred at a fine taxonomic scale. Here, we report two previously undescribed dinoflagellates, strains MGD and TGD, with green algal endosymbionts enclosing plastids as well as relic nuclei (nucleomorphs). We provide the evidence for the presence of DNA in the two nucleomorphs and transfer of endosymbiont genes to the host (dinoflagellate) genomes. Furthermore, DNA transfer between the host and endosymbiont nuclei was found to be in progress in both MGD and TGD systems. Phylogenetic analyses successfully resolved the origins of the endosymbionts at the genus level. Combined, we conclude that the host-endosymbiont integration in MGD/TGD is less advanced than that in cryptophytes/chrorarachniophytes, and propose the two dinoflagellates as new models for elucidating organellogenesis.

Background/Objectives: The aim of this study is to investigate the association between physical and chemical digestion and nutrition markers (serum albumin (ALB), prealbumin (PAB), and vitamin B12 (B12) levels). Methods: During a detailed checkup at Fujita Health University, we examined the associations of physical (occlusal force, masticatory performance, and swallowing ability (via the 10-item Eating Assessment Tool, EAT-10)) and chemical (Helicobacter pylori (HP) eradication history, HP antibody levels, and oral antacid (proton pump inhibitors) use) digestion parameters with serum ALB, PAB, and B12 levels in 92 individuals (M:67, F:25). Results: Forty-eight percent of the participants were older than 65 years of age, 19% had decreased occlusal force, 3.2% had decreased masticatory strength, 3.2% had decreased swallowing function, 24% had a history of HP eradication, 23% were HP antibody positive, and 16% were taking oral antacid medication. Additionally, 14% and 11% of the patients had low serum ALB and PAB levels, respectively, and 14% of the patients had B12 deficiency. Multivariate analysis adjusted for age, sex, body mass index, and C-reactive protein levels revealed that there were no significant associations between the physical digestion parameters and the serum PAB, ALB, or B12 levels. On the other hand, there was a significant association between oral antacid use and PAB levels (β = −3.3, p = 0.04). Independent of physical or chemical digestion parameters, serum PAB and B12 levels were significantly associated with protein and B12 intake, respectively. Conclusions: Oral antacid use may decrease serum PAB levels, indicating protein synthesis.