A resource of single-cell gene expression profiles in a planarian Dugesia japonica

The freshwater planarian Dugesia japonica maintains an abundant heterogeneous cell population called neoblasts, which include adult pluripotent stem cells. Thus, it is an excellent model organism for stem cell and regeneration research. Recently, many single-cell RNA sequencing (scRNA-seq) databases of several model organisms, including other planarian species, have become publicly available; these are powerful and useful resources to search for gene expression in various tissues and cells. However, the only scRNA-seq dataset for D. japonica has been limited by the number of genes detected. Herein, we collected D. japonica cells, and conducted an scRNA-seq analysis. A novel, automatic, iterative cell clustering strategy produced a dataset of 3,404 cells, which could be classified into 63 cell types based on gene expression profiles. We introduced two examples for utilizing the scRNA-seq dataset in this study using D. japonica. First, the dataset provided results consistent with previous studies as well as novel functionally relevant insights, that is, the expression of DjMTA and DjP2X-A genes in neoblasts that give rise to differentiated cells. Second, we conducted an integrative analysis of the scRNA-seq dataset and time-course bulk RNA-seq of irradiated animals, demonstrating that the dataset can help interpret differentially expressed genes captured via bulk RNA-seq. Using the R package “Seurat” and GSE223927, researchers can easily access and utilize this dataset.     

Identification and characterization of a fibroblast growth factor gene in the planarian Dugesia japonica

Planarians belong to the phylum Platyhelminthes and can regenerate their missing body parts after injury via activation of somatic pluripotent stem cells called neoblasts. Previous studies suggested that fibroblast growth factor (FGF) signaling plays a crucial role in the regulation of head tissue differentiation during planarian regeneration. To date, however, no FGF homologues in the Platyhelminthes have been reported. Here, we used a planarian Dugesia japonica model and identified an fgf gene termed Djfgf, which encodes a putative secreted protein with a core FGF domain characteristic of the FGF8/17/18 subfamily in bilaterians. Using Xenopus embryos, we found that DjFGF has FGF activity as assayed by Xbra induction. We next examined Djfgf expression in non-regenerating intact and regenerating planarians. In intact planarians, Djfgf was expressed in the auricles in the head and the pharynx. In the early process of regeneration, Djfgf was transiently expressed in a subset of differentiated cells around wounds. Notably, Djfgf expression was highly induced in the process of head regeneration when compared to that in the tail regeneration. Furthermore, assays of head regeneration from tail fragments revealed that combinatorial actions of the anterior extracellular signal-regulated kinase (ERK) and posterior Wnt/ß-catenin signaling restricted Djfgf expression to a certain anterior body part. This is the region where neoblasts undergo active proliferation to give rise to their differentiating progeny in response to wounding. The data suggest the possibility that DjFGF may act as an anterior counterpart of posteriorly localized Wnt molecules and trigger neoblast responses involved in planarian head regeneration.     

Characterization of tyramine beta-hydroxylase in planarian Dugesia japonica: cloning and expression

The planarian Dugesia japonica has a relatively well-organized central nervous system (CNS) consisting of a brain and ventral nerve cords (VNCs), and can completely regenerate it CNS utilizing pluripotent stem cells present in the mesenchymal space. This remarkable capacity has begun to be exploited for research on neural regeneration. Recently, several kinds of molecular markers for labeling of neural subtypes have been reported in planarians. These molecular markers are useful for visualizing the distinct neural populations in planarians. In this study, we isolated a cDNA encoding tyramine beta-hydroxylase (TBH), an octopamine (OA) biosynthetic enzyme, by degenerate PCR in the planarian D. japonica, and named it DjTBH (D. japonica tyramine beta-hydroxylase). In order to examine whether DjTBH contributes to OA biosynthesis, we measured the OA content in DjTBH-knockdown planarians created by RNA interference. In addition, to examine the specificity of DjTBH for OA biosynthesis, we measured not only OA content but also noradrenaline (NA) content, because NA is synthesized by a pathway similar to that for OA. According to high-performance liquid chromatography analysis, the amount of OA, but not NA, was significantly decreased in DjTBH-knockdown planarians. In addition, we produced anti-DjTBH antibody to visualize the octopaminergic neural network. As shown by immunofluorescence analysis using anti-DjTBH antibody, DjTBH-immunopositive neurons were mainly distributed in the head region, and elongated their dendrites and/or axons along the VNCs. In order to visualize octopaminergic and dopaminergic nervous systems (phenolamine/catecholamine nervous system) in the planarian CNS, double-immunofluorescence analysis was carried out using both anti-DjTBH antibody and anti-DjTH (a planarian tyrosine hydroxylase) antibody. DjTBH-immunopositive neurons and DjTH-immunopositive neurons mainly formed distinct neural networks in the head region. Here, we demonstrated that DjTBH clearly contributes to OA biosynthesis, and DjTBH antibody is a useful tool for detecting octopaminergic neurons in planarians.     

东亚三角涡虫Djtraf3基因的时空表达模式

肿瘤坏死因子受体相关因子3(TRAF3)作为TRAF家族的成员之一,通过介导TLRs信号通路,参与动物的免疫反应。通过构建东亚三角涡虫Djtraf3的cDNA文库获得Djtraf3基因并分析基因结构。结果发现,该最大开放阅读框为564bp,编码的蛋白质含187个氨基酸,含有1个TRAF结构域。进化分析表明,DjTRAF3和果蝇的TRAF3聚群,位于进化树的基部;整体原位杂交结果显示,在涡虫成体及不同再生阶段,Djtraf3在整个肠部表达。这些结果为进一步探究其功能提供了依据和方向。     

Structural analysis of N-glycans of the planarian Dugesia japonica

To investigate the relationship between phylogeny and glycan structures, we analyzed the structure of planarian N-glycans. The planarian Dugesia japonica, a member of the flatworm family, is a lower metazoan. N-glycans were prepared from whole worms by hydrazinolysis, followed by tagging with the fluorophore 2-aminopyridine at their reducing end. The labeled N-glycans were purified, and separated by three HPLC steps. By comparison with standard pyridylaminated N-glycans, it was shown that the N-glycans of planarian include high mannose-type and pauci-mannose-type glycans. However, many of the major N-glycans from planarians have novel structures, as their elution positions did not match those of the standard glycans. The results of mass spectrometry and sugar component analyses indicated that these glycans include methyl mannoses, and that the most probable linkage was 3-O-methylation. Furthermore, the methyl residues on the most abundant glycan may be attached to the non-reducing-end mannose, as the glycans were resistant to α-mannosidase digestion. These results indicate that methylated high-mannose-type glycans are the most abundant structure in planarians.     

Differentiation of epidermal cells in the regenerating planarian Dugesia japonica

Distribution of the cytoplasmic components in planarian epidermal cells is highly polarized, just as in vertebrate epithelia. Differentiating epidermal cells of the planarian Dugesia japonica Ichikawa et Kawakatsu were found to have relatively conspicuous accumulations of microtubules in their apical cytoplasm. When colchicine, a microtubule-disrupting drug, was applied to regenerating worms, it reversibly disorganized the polarity of differentiating epidermal cells. Cytochalasin B, which depolymerizes actin filaments, had no significant effect on the polarization, however. Tubulin could be localized by immunocytochemistry in the cytoplasm of differentiating epidermal cells; this reaction was inhibited by treatment with colchicine for 20 h. These observations indicate that microtubules play a role in establishing polarity during cell differentiation.     

东亚三角涡虫胰蛋白酶Djtry的表达和酶活分析

通过对东亚三角涡虫胰蛋白酶Djtry氨基酸序列比对分析,发现保守的催化三联体结构中第一位的His被Lys所取代。为了探究这种突变是否会对胰蛋白酶的活性有影响,文章构建了原核表达重组质粒pET-28a-Djtry,转化到E.coli BL21中,利用IPTG诱导表达,对表达的重组蛋白进行变性、复性、纯化以及Westernblotting鉴定,获得成分均一的活性蛋白。利用牛胰蛋白酶为标准品,胰蛋白酶特异性底物BAEE,检测Djtry酶活力与比活力。SDS-PAGE电泳表明诱导表达的融合蛋白为包涵体,分子量约为26 kDa,Western blotting结果显示为目的蛋白,对复性纯化的目的蛋白进行酶活检测发现,突变型胰蛋白酶Djtry仍然保持了胰蛋白酶催化性质,但是催化活性相对较弱。     

东亚三角涡虫胰蛋白酶Djtry的表达和酶活分析

通过对东亚三角涡虫胰蛋白酶Djtry氨基酸序列比对分析, 发现保守的催化三联体结构中第一位的His被Lys所取代。为了探究这种突变是否会对胰蛋白酶的活性有影响, 文章构建了原核表达重组质粒pET-28a- Djtry, 转化到E.coli BL21中, 利用IPTG诱导表达, 对表达的重组蛋白进行变性、复性、纯化以及Western blotting鉴定, 获得成分均一的活性蛋白。利用牛胰蛋白酶为标准品, 胰蛋白酶特异性底物BAEE, 检测Djtry酶活力与比活力。SDS-PAGE电泳表明诱导表达的融合蛋白为包涵体, 分子量约为26 kDa, Western blotting结果显示为目的蛋白, 对复性纯化的目的蛋白进行酶活检测发现, 突变型胰蛋白酶Djtry仍然保持了胰蛋白酶催化性质, 但是催化活性相对较弱。     

Regulation of intermediate filament gene expression.

Members of the intermediate filament protein family exhibit complex patterns of development-specific and tissue-specific expression. Studies exploring the mechanisms of gene regulation are underway and key regulatory factors are currently being described and isolated for certain genes encoding intermediate filament proteins. Selected systems from this diverse group of about 50 genes will be discussed.     

Identification of small non-coding RNAs in the planarian Dugesia japonica via deep sequencing

Freshwater planarian flatworm possesses an extraordinary ability to regenerate lost body parts after amputation; it is perfect organism model in regeneration and stem cell biology. Recently, small RNAs have been an increasing concern and studied in many aspects, including regeneration and stem cell biology, among others. In the current study, the large-scale cloning and sequencing of sRNAs from the intact and regenerative planarian Dugesia japonica are reported. Sequence analysis shows that sRNAs between 18nt and 40nt are mainly microRNAs and piRNAs. In addition, 209 conserved miRNAs and 12 novel miRNAs are identified. Especially, a better screening target method, negative-correlation relationship of miRNAs and mRNA, is adopted to improve target prediction accuracy. Similar to miRNAs, a diverse population of piRNAs and changes in the two samples are also listed. The present study is the first to report on the important role of sRNAs during planarian Dugesia japonica regeneration.     

A fine structural study of regeneration after fission in the planarian Dugesia japonica

We examined morphologically the process of regeneration before and after fission in a sexual strain of the freshwater planarian Dugesia japonica. Usually fission takes place in the post-pharyngeal region. Decapitation significantly accelerates the rate of fissioning. When decapitated worms were treated with substance P and neuropeptide K separately, the rate of fission markedly decreased in both cases. Before the onset of fission, a presumptive region of fission was recognized in the post-pharyngeal portion where undifferentiated cells, regenerative cells and newly differentiated cells were localized. Moreover a functional network of fixed parenchyma cells was noted in this region. After fission, cell distribution in the blastema became quite different from that of artificially amputated worms. This difference seems to be due to the process that occurs in the presumptive region of fission. This revised version was published online in July 2006 with corrections to the Cover Date.     

Anatomy of the planarian Dugesia japonica I. The muscular system revealed by antisera against myosin heavy chains

The planarian Dugesia japonica has two genes encoding myosin heavy chain, DjMHC-A and B (Kobayashi et al., 1998). We produced antibodies specifically recognizing each myosin heavy chain protein using their carboxyl terminal regions expressed in E. coli as antigens. Immunohistochemical analyses of sections and whole-mount specimens revealed the detailed structure and distribution of each type of muscle fiber in the planarian. In general, the MHC-A muscle fibers were distributed beneath the epithelial layers, namely, they were observable in the pharynx, the mouth, the intestine, the eyes and the body wall. In the pharynx, only MHC-A muscle fibers were present. In contrast, the MHC-B muscle fibers were distributed in the mesenchyme as dorso-ventral and transverse muscles, and in the body wall. The body-wall muscles were composed of an outer layer of circular MHC-A muscles and inner longitudinal and intermediate diagonal MHC-B muscle layers. Thus, two types of muscle fibers were distinguished by their distribution in the planarian.     

Bone morphogenetic protein is required for dorso-ventral patterning in the planarian Dugesia japonica

In order to clarify the function of the Djbmp (Dugesia japonica bone morphogenetic protein) gene in planarian body patterning, we carried out knockdown of this gene by RNA interference. When the planarians were treated with double-stranded RNA of Djbmp, a bulge formed on the dorsal side, with a dent in the middle of the bulge, and the body surface inside the dent was smoothened and less pigmented. In situ hybridization of the DjIFb gene, which is expressed in the body margin, revealed that the additional body margin was formed ectopically at the region surrounding the dent. The Djbmp-knockdown planarians often had a pair of incomplete nerve cords in the dorsal side, in addition to the original pair of ventral nerve cords. Taken together, we concluded that the Djbmp-knockdown induced formation of an ectopic ventral side, suggesting that Djbmp is required for the dorso-ventral body patterning in the planarian.     

Role of fixed parenchyma cells in blastema formation of the planarian Dugesia japonica.

Observations of fixed parenchyma cells using electron microscopy were carried out in an attempt to understand the morphogenetic process of blastema formation in regenerating planarians. Fixed parenchyma cells could be found throughout one-day blastemata. In the mid-blastema region where migrating regenerative cells build up a compact cell aggregate, long and slender cytoplasmic processes of the fixed parenchyma cells were seen occupying spaces among regenerative cells. A characteristic feature of such processes was orderly arranged microtubules. Ruthenium red staining revealed thickened portions of cell coats on these processes and occasional formation of gap junctions between the cytoplasmic process of the fixed parenchyma cell and the regenerative cell undergoing migration. Colchicine treatment (M/1,000) caused detachment of the cytoplasmic processes from the regenerative cells. Microtubules within such processes became depolymerized. As a result, directional migration of regenerative cells was inhibited by colchicine treatment. To determine the extracellular site of fibronectin, immunoelectron microscopy was performed in one-day blastema. Immunogold labeling was detected at the surface area of fixed parenchyma cells and regenerative cells. In particular the reactivity was conspicuous at the cytoplasmic process of the fixed parenchyma cells. These observations suggest that the cytoplasmic processes of fixed parenchyma cell are related to directional movement of regenerative cells by providing a contact guidance system. The biological implications of this system are discussed in relation to the extracellular matrix components.     

Ultrastructural observations on gastrodermal regeneration in the planarian Dugesia japonica (Turbellaria)

The earliest detectable change during regeneration of the gastrodermis in Dugesia japonica was an aggregation of regenerative cells underneath the gastrodermis remaining at the wound margin. The gastrodermal cells in experimental regenerates retained some of their original characters and presented no indication of cell dedifferentiation. The regenerative cells came into contact with the basal surface of gastrodermal cells, forming stratified cell layers. Differentiation of these cells into gastrodermal cells was initiated by the development of synthetic organelles within their cytoplasm. These differentiating cells gave rise to two different types of gastrodermal cells, namely phagocytic cells and sphere cells. In later stages, there was an apparent movement of differentiated gastrodermal cells towards the parenchyma.     

Heterogeneity of chromatoid bodies in adult pluripotent stem cells of planarian Dugesia japonica

The robust regenerative ability of planarians is known to be dependent on adult pluripotent stem cells called neoblasts. One of the morphological features of neoblasts is cytoplasmic ribonucleoprotein granules (chromatoid bodies: CBs), which resemble germ granules present in germline cells in other animals. Previously, we showed by immuno‐electron microscopic analysis that DjCBC‐1, a planarian Me31B/Dhh1/DDX6 homologue, which is a component of ribonucleoprotein granules, was localized in CBs in the planarian Dugesia japonica. Also, recently it was reported using another planarian species that Y12 antibody recognizing symmetrical dimethylarginine (sDMA) specifically binds to CBs in which histone mRNA is co‐localized. Here, we showed by double immunostaining and RNA interference (RNAi) that DjCBC‐1‐containing CBs and Y12‐immunoreactive CBs are distinct structures, suggesting that CBs are composed of heterogeneous populations. We also found that the Y12‐immunoreactive CBs specifically contained a cytoplasmic type of planarian PIWI protein (DjPiwiC). We revealed by RNAi experiments that Y12‐immunoreactive CBs may have anti‐transposable element activity involving the DjPiwiC protein in the neoblasts.