Hiroshi Kagoshima

RUNX regulates stem cell proliferation and differentiation: Insights from studies of C. elegans

The RUNX genes encode conserved transcription factors that play vital roles in the development of various animals and human diseases. Recent studies by a few groups including ours have demonstrated that this gene family, as represented by a single ortholog designeated rnt‐1, also occurs and plays intriguing roles in the simple model organism, Caenorhabditis elegans. Our genetic and molecular analyses revealed that rnt‐1 is allelic to mab‐2, which had previously been known to cause an abnormal development of the male tail. rnt‐1 was further shown to be predominantly expressed in the stem cell‐like lateral seam hypodermal cells. These cells are characterized by their abilities to undergo stem cell‐like asymmetric divisions giving rise to self‐renewing seam cells and various differentiated descendants of hypodermal and neuronal fates. We found that rnt‐1 mutants exhibit an impaired asymmetry in the division of T cells, the posterior‐most member of the seam cells. Mutant analysis indicated that rnt‐1 is involved in regulating T blast cell polarity in cooperation with the Wnt signaling pathway. On the other hand, Nimmo et al. independently discovered that rnt‐1 acts as a rate limiting regulator of cell proliferation in the seam cells, V1‐6. In this review, we will outline these new findings and discuss their general implications in the mechanism of coordination between proliferation and differentiation of stem cells. J. Cell. Biochem. 100: 1119–1130, 2007.

Microflorae of aquatic moss pillars in a freshwater lake, East Antarctica, based on fatty acid and 16S rRNA gene analyses

Aquatic mosses in the genera Bryum and Leptobryum form unique tower-like “moss pillars” underwater in some Antarctic lakes, in association with algae and cyanobacteria. These are communities with a two-layer structure comprising an oxidative exterior and reductive interior. Although habitats and photosynthetic properties of moss pillars have been reported, microfloral composition of the two-layer structure has not been described. Here we report fatty acid analysis of one moss pillar and molecular phylogenetic analysis, based on the 16S rRNA gene, of this and one other moss pillar. Cluster analysis of the phospholipid fatty acid composition showed three groups corresponding to the exterior, upper interior, and lower interior of the pillar. This suggested that species composition differed by section, with the exterior dominated by photosynthetic organisms such as mosses, algae, and cyanobacteria, the upper interior primarily containing gram-positive bacteria and anaerobic sulfate-reducing bacteria, and the lower interior dominated by gram-negative bacteria. Molecular phylogenetic analysis revealed that Proteobacteria dominate the moss pillar as a whole; cyanobacteria were found on the exterior and the gram-positive obligate anaerobe Clostridium in the interior, while gram-positive sulfate-reducing bacteria were present in the lowest part of the interior. Nitrogen-fixing bacteria and denitrifying bacteria were found in all sections. Thus, fatty acid analysis and genetic analysis showed similar patterns. These findings suggest that microorganisms of different phylogenetic groups inhabit different sections of a single moss pillar and form a microbial community that performs biogeochemical cycling to establish and maintain a structure in an oxidation–reduction gradient between exterior and interior.

Eukaryotic phylotypes in aquatic moss pillars inhabiting a freshwater lake in East Antarctica, based on 18S rRNA gene analysis

Aquatic mosses of Leptobryum species form unique tower-like pillars of vegetation termed “moss pillars” in Antarctic lakes. Moss pillars have distinct redox-affected sections: oxidative exteriors and reductive interiors. We have proposed that a “pillar” is a community and habitat of functionally interdependent organisms and may represent a mini-biosphere. Batteries of 16S rRNA genotypes, or phylotypes, of eubacteria and cyanobacteria, but no archaea, have been identified in moss pillars. However, detailed identification or phylogenetic analyses of the moss and their associated eukaryotic microbiota have not been performed. This study analyzed near-full-length 18S rRNA gene sequences obtained from two whole moss pillars. In total, 28 PCR clone libraries from two whole moss pillars were constructed, and 96 clones from each library (total 2,688 clones) were randomly selected and sequenced. Molecular phylogenetic analysis revealed that the phylotype belonging to Bryophyta, considered to be derived from moss, was closely related (99.9xa0%) to the 18S rRNA gene sequence from Leptobryum pyriforme. Unexpectedly, phylotypes belonging to a novel clade of fungi dominated (approximately 27–75xa0%) the moss pillar libraries. This suggests that fungi may contribute to carbon cycling in the moss pillar as parasites or decomposers. In addition, phylotypes related to ciliates and tardigrades were subdominant in the exterior, while the phylotype of the ameba-like, single-celled eukaryote, Cercomonas (Cercozoa), was detected only in the interior. These features were shared by both moss pillars. The 18S rRNA gene-based profiles demonstrated that redox-related factors may control distribution of some eukaryotic microbes in a whole moss pillar.

Comparative genome and transcriptome analyses of the social amoeba Acytostelium subglobosum that accomplishes multicellular development without germ-soma differentiation

BackgroundSocial amoebae are lower eukaryotes that inhabit the soil. They are characterized by the construction of a starvation-induced multicellular fruiting body with a spore ball and supportive stalk. In most species, the stalk is filled with motile stalk cells, as represented by the model organism Dictyostelium discoideum, whose developmental mechanisms have been well characterized. However, in the genus Acytostelium, the stalk is acellular and all aggregated cells become spores. Phylogenetic analyses have shown that it is not an ancestral genus but has lost the ability to undergo cell differentiation.ResultsWe performed genome and transcriptome analyses of Acytostelium subglobosum and compared our findings to other available dictyostelid genome data. Although A. subglobosum adopts a qualitatively different developmental program from other dictyostelids, its gene repertoire was largely conserved. Yet, families of polyketide synthase and extracellular matrix proteins have not expanded and a serine protease and ABC transporter B family gene, tagA, and a few other developmental genes are missing in the A. subglobosum lineage. Temporal gene expression patterns are astonishingly dissimilar from those of D. discoideum, and only a limited fraction of the ortholog pairs shared the same expression patterns, so that some signaling cascades for development seem to be disabled in A. subglobosum.ConclusionsThe absence of the ability to undergo cell differentiation in Acytostelium is accompanied by a small change in coding potential and extensive alterations in gene expression patterns.

Genome analysis of Diploscapter coronatus : insights into molecular peculiarities of a nematode with parthenogenetic reproduction

BackgroundSexual reproduction involving the fusion of egg and sperm is prevailing among eukaryotes. In contrast, the nematode Diploscapter coronatus, a close relative of the model Caenorhabditis elegans, reproduces parthenogenetically. Neither males nor sperm have been observed and some steps of meiosis are apparently skipped in this species. To uncover the genomic changes associated with the evolution of parthenogenesis in this nematode, we carried out a genome analysis.ResultsWe obtained a 170 Mbp draft genome in only 511 scaffolds with a N50 length of 1 Mbp. Nearly 90% of these scaffolds constitute homologous pairs with a 5.7% heterozygosity on average and inversions and translocations, meaning that the 170 Mbp sequences correspond to the diploid genome. Fluorescent staining shows that the D. coronatus genome consists of two chromosomes (2nxa0=xa02). In our genome annotation, we found orthologs of 59% of the C. elegans genes. However, a number of genes were missing or very divergent. These include genes involved in sex determination (e.g. xol-1, tra-2) and meiosis (e.g. the kleisins rec-8 and coh-3/4) giving a possible explanation for the absence of males and the second meiotic division. The high degree of heterozygosity allowed us to analyze the expression level of individual alleles. Most of the homologous pairs show very similar expression levels but others exhibit a 2–5-fold difference.ConclusionsOur high-quality draft genome of D. coronatus reveals the peculiarities of the genome of parthenogenesis and provides some clues to the genetic basis for parthenogenetic reproduction. This draft genome should be the basis to elucidate fundamental questions related to parthenogenesis such as its origin and mechanisms through comparative analyses with other nematodes. Furthermore, being the closest outgroup to the genus Caenorhabditis, the draft genome will help to disclose many idiosyncrasies of the model C. elegans and its congeners in future studies.

Diversity of RuBisCO gene responsible for CO2 fixation in an Antarctic moss pillar

Antarctic “moss pillars” are lake-bottom biocenoses that are primarily comprised of aquatic mosses. The pillars consist of distinct redox-affected sections: oxidative exteriors and reductive interiors. Batteries of SSU rRNA genotypes of eukaryotes, eubacteria, and cyanobacteria, but no archaea, have been identified in these pillars. However, rRNA-based phylogenetic analysis provides limited information on metabolic capabilities. To investigate the microorganisms that have the potential for CO2 fixation in the pillars, we studied the genetic diversity of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO, EC 4.1.1.39)—an enzyme involved in CO2 fixation. PCR clone libraries targeting all forms of the RuBisCO large subunit-encoding gene were constructed and 1,092 clones were randomly sequenced. Phylogenetic analysis indicated that proteobacterial form IA operational RuBisCO units (ORUs) were detected at the same frequency as the cyanobacterial form IB ORUs. Surprisingly, the form IA ORU, which was closely related to the sequences from deep-sea environments, was detected from all moss pillar sections. The form IB ORU related to Bryophyta, considered to be derived from moss, was identical to the sequence of Leptobryum sp. isolated from Lake Hotoke-Ike where the pillars were found. Moreover, certain cyanobacterial ORUs were found exclusively in the exterior of the pillar, whereas form II ORUs related to chemolithoautotrophic sulfur oxidizers and purple sulfur bacteria were found exclusively in the interior. No forms IC, ID, or III RuBisCO genes were detected. This is the first report demonstrating that bacteria with the potential for CO2 fixation and chemoautotrophy are present in the Antarctic moss pillar ecosystem.

The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization

Land plants evolved from charophytic algae, among which Charophyceae possess the most complex body plans. We present the genome of Chara braunii; comparison of the genome to those of land plants identified evolutionary novelties for plant terrestrialization and land plant heritage genes. C.xa0braunii employs unique xylan synthases for cell wall biosynthesis, a phragmoplast (cell separation) mechanism similar to that of land plants, and many phytohormones. C.xa0braunii plastids are controlled via land-plant-like retrograde signaling, and transcriptional regulation is more elaborate than in other algae. The morphological complexity of this organism may result from expanded gene families, with three cases of particular note: genes effecting tolerance to reactive oxygen species (ROS), LysM receptor-like kinases, and transcription factors (TFs). Transcriptomic analysis of sexual reproductive structures reveals intricate control by TFs, activity of the ROS gene network, and the ancestral use of plant-like storage and stress protection proteins in the zygote.

Meiofaunal Richness in Highly Acidic Hot Springs in Unzen-Amakusa National Park, Japan, Including the First Rediscovery Attempt for Mesotardigrada.

Extreme environments sometimes support surprisingly high meiofaunal diversity. We sampled runoff from the acidic hot springs of Unzen, Japan. This is the type locality of Thermozodium esakii Rahm, 1937, the only tardigrade in the class Mesotardigrada, which remains contentious in the absence of corroboration or supporting specimens. Our sampling revealed at least three species of arthropods, four rotifers, and five nematodes living in the hot (ca. 40°C) and acidic (ca. pH 2.5) water, but no tardigrades.

Co-expression of the transcription factors CEH-14 and TTX-1 regulates AFD neuron-specific genes gcy-8 and gcy-18 in C. elegans.

A wide variety of cells are generated by the expression of characteristic sets of genes, primarily those regulated by cell-specific transcription. To elucidate the mechanism regulating cell-specific gene expression in a highly specialized cell, AFD thermosensory neuron in Caenorhabditis elegans, we analyzed the promoter sequences of guanylyl cyclase genes, gcy-8 and gcy-18, exclusively expressed in AFD. In this study, we showed that AFD-specific expression of gcy-8 and gcy-18 requires the co-expression of homeodomain proteins, CEH-14/LHX3 and TTX-1/OTX1. We observed that mutation of ttx-1 or ceh-14 caused a reduction in the expression of gcy-8 and gcy-18 and that the expression was completely lost in double mutants. This synergy effect was also observed with other AFD marker genes, such as ntc-1, nlp-21and cng-3. Electrophoretic mobility shift assays revealed direct interaction of CEH-14 and TTX-1 proteins with gcy-8 and gcy-18 promoters in vitro. The binding sites of CEH-14 and TTX-1 proteins were confirmed to be essential for AFD-specific expression of gcy-8 and gcy-18 in vivo. We also demonstrated that forced expression of CEH-14 and TTX-1 in AWB chemosensory neurons induced ectopic expression of gcy-8 and gcy-18 reporters in this neuron. Finally, we showed that the regulation of gcy-8 and gcy-18 expression by ceh-14 and ttx-1 is evolutionally conserved in five Caenorhabditis species. Taken together, ceh-14 and ttx-1 expression determines the fate of AFD as terminal selector genes at the final step of cell specification.

Gilbert Rahm and the status of Mesotardigrada Rahm, 1937

The tardigrade class Mesotardigrada was erected on the basis of the description of Thermozodium esakii by Gilbert Rahm in 1937. In some characteristics, T. esakii is intermediate between members of the classes Eutardigrada and Heterotardigrada. The class Mesotardigrada is known only from Rahms published drawings of T. esakii; no voucher specimens are known, and subsequent attempts to collect it at the locus typicus have been unsuccessful. Among the possible explanations for this situation are that Rahm may have collected specimens of a more typical tardigrade, but misinterpreted what he saw. Alternatively, changes in habitat in the area may have led to the tardigrades extirpation. Perhaps T. esakii is a rare species, such that recent sampling efforts have been insufficient to rediscover it. Finally, Rahms 1937 description may be an attempt at deception. Until physical evidence of T. esakii is found, the species, and by extension the class Mesotardigrada, should be considered nomen dubium.