A Comprehensive Transcriptomic and Proteomic Analysis of Hydra Head Regeneration

The cnidarian freshwater polyp Hydra sp. exhibits an unparalleled regeneration capacity in the animal kingdom. Using an integrative transcriptomic and stable isotope labeling by amino acids in cell culture proteomic/phosphoproteomic approach, we studied stem cell-based regeneration in Hydra polyps. As major contributors to head regeneration, we identified diverse signaling pathways adopted for the regeneration response as well as enriched novel genes. Our global analysis reveals two distinct molecular cascades: an early injury response and a subsequent, signaling driven patterning of the regenerating tissue. A key factor of the initial injury response is a general stabilization of proteins and a net upregulation of transcripts, which is followed by a subsequent activation cascade of signaling molecules including Wnts and transforming growth factor (TGF) beta-related factors. We observed moderate overlap between the factors contributing to proteomic and transcriptomic responses suggesting a decoupled regulation between the transcriptional and translational levels. Our data also indicate that interstitial stem cells and their derivatives (e.g., neurons) have no major role in Hydra head regeneration. Remarkably, we found an enrichment of evolutionarily more recent genes in the early regeneration response, whereas conserved genes are more enriched in the late phase. In addition, genes specific to the early injury response were enriched in transposon insertions. Genetic dynamicity and taxon-specific factors might therefore play a hitherto underestimated role in Hydra regeneration.

A novel neuropeptide (FRamide) family identified by a peptidomic approach in Hydra magnipapillata

In the course of systematic identification of peptide signaling molecules combined with the expressed sequence tag database from Hydra, we have identified a novel neuropeptide family that consists of two members with FRamide at the C-terminus; FRamide-1 (IPTGTLIFRamide) and FRamide-2 (APGSLLFRamide). The precursor sequence deduced from cDNA contained a single copy each of FRamide-1 and FRamide-2 precursor sequences. Expression analysis by whole-mount in situ hybridization showed that the gene was expressed in a subpopulation of neurons that were distributed throughout the body from tentacles to basal disk. Double in situ hybridization analysis showed that the expressing cell population was further subdivided into one population consisting of neurons expressing both the FRamide and Hym176 (neuropeptide) genes and the other consisting of neurons expressing only the FRamide gene. FRamide-1 evoked elongation of the body column of 'epithelial' Hydra that was composed of epithelial cells and gland cells but lacked all the cells in the interstitial stem cell lineage, including neurons. In contrast, FRamide-2 evoked body column contraction. These results suggest that both of the neuropeptides directly act on epithelial cells as neurotransmitters and regulate body movement in an axial direction.

The evolutionary emergence of cell type-specific genes inferred from the gene expression analysis of Hydra

Cell lineages of cnidarians including Hydra represent the fundamental cell types of metazoans and provides us a unique opportunity to study the evolutionary diversification of cell type in the animal kingdom. Hydra contains epithelial cells as well as a multipotent interstitial cell (I-cell) that gives rise to nematocytes, nerve cells, gland cells, and germ-line cells. We used cDNA microarrays to identify cell type-specific genes by comparing gene expression in normal Hydra with animals lacking the I-cell lineage, so-called epithelial Hydra. We then performed in situ hybridization to localize expression to specific cell types. Eighty-six genes were shown to be expressed in specific cell types of the I-cell lineage. An additional 29 genes were expressed in epithelial cells and were down-regulated in epithelial animals lacking I-cells. Based on the above information, we constructed a database (http://hydra.lab.nig.ac.jp/hydra/), which describes the expression patterns of cell type-specific genes in Hydra. Most genes expressed specifically in either I-cells or epithelial cells have homologues in higher metazoans. By comparison, most nematocyte-specific genes and approximately half of the gland cell- and nerve cell-specific genes are unique to the cnidarian lineage. Because nematocytes, gland cells, and nerve cells appeared along with the emergence of cnidarians, this suggests that lineage-specific genes arose in cnidarians in conjunction with the evolution of new cell types required by the cnidarians.

Universal occurrence of the vasa-related genes among metazoans and their germline expression in Hydra

The vasa (vas)-related genes are members of the DEAD box protein family and are involved in germ cell formation in higher metazoans. In the present study, we cloned the vas-related genes as well as the PL10-related genes, other members of the DEAD box protein family, from lower metazoans: sponge, Hydra and planaria. The phylogenetic analysis suggested that the vas-related genes arose by duplication of a PL10-related gene before the appearance of sponges but after the diversion of fungi and plants. The vas-related genes in Hydra, Cnvas1 and Cnvas2 were strongly expressed in germline cells and less strongly expressed in multipotent interstitial stem cells and ectodermal epithelial cells. These results suggest that the vas-related genes occur universally among metazoans and that their expression in germline cells was established at least before cnidarian evolution.

Expression and evolutionary conservation of nanos-related genes in Hydra

The Drosophila gene nanos encodes two particular zinc finger motifs which are also found in germline-associated factors from nematodes to vertebrates. We cloned two nanos (nos)-related genes, Cnnos1 and Cnnos2 from Hydra magnipapillata. Using whole-mount in situ hybridization, the expression of Cnnos1 and Cnnos2 was examined. Cnnos1 was specifically expressed in multipotent stem cells and germline cells, but not in somatic cells. Cnnos2 was weakly expressed in germline cells and more specifically in the endoderm of the hypostome where it appears to be involved in head morphogenesis. In addition to structural conservation in the zinc finger domain of nanos-related genes, functional conservation of Cnnos1 was also demonstrated by the finding that a Cnnos1 transgene can partially rescue the nosRC phenotype that is defective in the egg production of Drosophila. Thus, the function of nanos-related genes in the germline appears to be well conserved from primitive to highly evolved metazoans.

Genetic analysis of developmental mechanisms in Hydra. XXII. Two types of female germ stem cells are present in a male strain of Hydra magnipapillata

Three types of interstitial stem cell subpopulation were isolated from Hydra magnipapillata, and their roles in sex determination were examined. A subpopulation of interstitial stem cells restricted to the sperm differentiation pathway was isolated previously from strain nem-1 (male). Another subpopulation restricted to the egg differentiation pathway was also isolated from the same strain. Hydroxyurea treatment was used for isolation in both cases. "Pseudoepithelial hydra" containing only sperm- or egg-restricted stem cell but no other interstitial stem cell types were maintained by force-feeding for 2 years. Sex reversal from egg- to sperm-restricted stem cells occurred three times during this period. Both of these two stem cell types are numerous in the central gastric region of the pseudoepithelial hydra, but absent in the foot region below the budding zone. Foot tissue was cut out from normal nem-1 polyps (male) and allowed to regenerate. The regenerates produced eggs but no sperm upon sex induction. These and other results suggest that the foot tissue contains multipotent stem cells capable of differentiating into eggs during sexual differentiation. These observations suggest that strain nem-1 (male) contains three types of interstitial stem cell subpopulations: (1) sperm-restricted stem cells, (2) egg-restricted stem cells, and (3) multipotent stem cells capable of differentiating into nerve cells, nematocytes, and eggs. Upon sex induction, however, differentiation of eggs by the latter two types is suppressed, and only sperm are produced by the sperm-restricted stem cells. Evidence is presented which suggests that similar "phenotypic males," which normally only produce sperm but contain the stem cell types capable of differentiating into eggs, occur widely in Hydra magnipapillata. A possible relationship between phenotypic male hydra and hermaphroditic hydra is discussed.

Genetic analysis of developmental mechanisms in hydra. XX. Cloning of interstitial stem cells restricted to the sperm differentiation pathway in Hydra magnipapillata

Hydra magnipapillata polyps containing a subpopulation of interstitial stem cells restricted to the germline differentiation pathway were obtained. Chim-C1 is a chimeric strain produced by combining wild-type epithelial cell lineages with a temperature-sensitive interstitial cell lineage. It grows normally at 18 degrees C. When cultured at 25 degrees C, many polyps lost interstitial cells and their differentiation products (nerve cells and nematocytes), and subsequently turned into epithelial hydra unable to move or feed. Some polyps, however, turned into an unexpected type, termed "pseudo-epithelial hydra." These polyps resembled epithelial hydra in the absence of nerve cells or nematocytes in the tissue and in their inability to move or feed. In contrast to epithelial hydra, however, their tissue contained proliferating interstitial cells. Similar pseudo-epithelial hydra were also produced from another strain, nem-1, by means of hydroxyurea treatment. Clones of pseudo-epithelial hydra were maintained through force-feeding over 130 days for chim-C1 and over 2 years for nem-1. In both cases, interstitial cells proliferated throughout the period without producing any nerve cells or nematocytes. These interstitial cells, however, differentiated into sperm. Thus, the interstitial cells present in pseudo-epithelial hydra were able to differentiate into gametic cells but not into somatic cells (nerve cells and nematocytes). These observations suggest that, as Littlefield (1985, Dev. Biol. 112, 185-193) has shown for H. oligactis, the interstitial stem cell population in H. magnipapillata includes a subpopulation which can differentiate only into gametic cells.