'Guessmer' screening strategy applied to species with AT-rich coding sequences

The state of Medusozoa genomics: current evidence and future challenges

Medusozoa is a widely distributed ancient lineage that harbors one-third of Cnidaria diversity divided into 4 classes. This clade is characterized by the succession of stages and modes of reproduction during metagenic lifecycles, and includes some of the most plastic body plans and life cycles among animals. The characterization of traditional genomic features, such as chromosome numbers and genome sizes, was rather overlooked in Medusozoa and many evolutionary questions still remain unanswered. Modern genomic DNA sequencing in this group started in 2010 with the publication of the Hydra vulgaris genome and has experienced an exponential increase in the past 3 years. Therefore, an update of the state of Medusozoa genomics is warranted. We reviewed different sources of evidence, including cytogenetic records and high-throughput sequencing projects. We focused on 4 main topics that would be relevant for the broad Cnidaria research community: (i) taxonomic coverage of genomic information; (ii) continuity, quality, and completeness of high-throughput sequencing datasets; (iii) overview of the Medusozoa specific research questions approached with genomics; and (iv) the accessibility of data and metadata. We highlight a lack of standardization in genomic projects and their reports, and reinforce a series of recommendations to enhance future collaborative research.

Signalling by the FGFR-like tyrosine kinase, Kringelchen, is essential for bud detachment in Hydra vulgaris

Signalling through fibroblast growth factors (FGFR) is essential for proper morphogenesis in higher evolved triploblastic organisms. By screening for genes induced during morphogenesis in the diploblastic Hydra, we identified a receptor tyrosine kinase (kringelchen) with high similarity to FGFR tyrosine kinases. The gene is dynamically upregulated during budding, the asexual propagation of Hydra. Activation occurs in body regions, in which the intrinsic positional value changes. During tissue displacement in the early bud, kringelchen RNA is transiently present ubiquitously. A few hours later – coincident with the acquisition of organiser properties by the bud tip – a few cells in the apical tip express the gene strongly. About 20 hours after the onset of evagination, expression is switched on in a ring of cells surrounding the bud base, and shortly thereafter vanishes from the apical expression zone. The basal ring persists in the parent during tissue contraction and foot formation in the young polyp, until several hours after bud detachment. Inhibition of bud detachment by head regeneration results in severe distortion, disruption or even complete loss of the well-defined ring-like expression zone. Inhibition of FGFR signalling by SU5402 or, alternatively, inhibition of translation by phosphorothioate antisense oligonucleotides inhibited detachment of buds, indicating that, despite the dynamic expression pattern,the crucial phase for FGFR signalling in Hydra morphogenesis lies in bud detachment. Although Kringelchen groups with the FGFR family, it is not known whether this protein is able to bind FGFs, which have not been isolated from Hydra so far.

Cnidarian and bilaterian promoters can direct GFP expression in transfected hydra

Complete sexual development is not easily amenable to experimentation in hydra. Therefore, the analysis of gene function and gene regulation requires the introduction of exogenous DNA in a large number of cells of the hydra polyps and the significant expression of reporter constructs in these cells. We present here the procedure whereby we coupled DNA injection into the gastric cavity to electroporation of the whole animal in order to efficiently transfect hydra polyps. We could detect GFP fluorescence in both endodermal and ectodermal cell layers of live animals and in epithelial as well as interstitial cell types of dissociated hydra. In addition, we could confirm GFP protein expression by showing colocalisation between GFP fluorescence and anti-GFP immunofluorescence. Finally, when a FLAG epitope was inserted in-frame with the GFP coding sequence, GFP fluorescence also colocalised with anti-FLAG immunofluorescence. This GFP expression in hydra cells was directed by various promoters, either homologous, like the hydra homeobox cnox-2 gene promoter, or heterologous, like the two nematode ribosomal protein S5 and L28 gene promoters, and the chicken beta-actin gene promoter. This strategy provides new tools for dissecting developmental molecular mechanisms in hydra; more specifically, the genetic regulations that take place in endodermal cells at the time budding or regeneration is initiated.

Evolution of Antp-class genes and differential expression of Hydra Hox/paraHox genes in anterior patterning

The conservation of developmental functions exerted by Antp-class homeoproteins in protostomes and deuterostomes suggested that homologs with related functions are present in diploblastic animals. Our phylogenetic analyses showed that Antp-class homeodomains belong either to non-Hox or to Hox/paraHox families. Among the 13 non-Hox families, 9 have diploblastic homologs, Msx, Emx, Barx, Evx, Tlx, NK-2, and Prh/Hex, Not, and Dlx, reported here. Among the Hox/paraHox, poriferan sequences were not found, and the cnidarian sequences formed at least five distinct cnox families. Two are significantly related to the paraHox Gsx (cnox-2) and the mox (cnox-5) sequences, whereas three display some relatedness to the Hox paralog groups 1 (cnox-1), 9/10 (cnox-3) and the paraHox cdx (cnox-4). Intermediate Hox/paraHox genes (PG 3 to 8 and lox) did not have clear cnidarian counterparts. In Hydra, cnox-1, cnox-2, and cnox-3 were not found chromosomally linked within a 150-kb range and displayed specific expression patterns in the adult head. During regeneration, cnox-1 was expressed as an early gene whatever the polarity, whereas cnox-2 was up-regulated later during head but not foot regeneration. Finally, cnox-3 expression was reestablished in the adult head once it was fully formed. These results suggest that the Hydra genes related to anterior Hox/paraHox genes are involved at different stages of apical differentiation. However, the positional information defining the oral/aboral axis in Hydra cannot be correlated strictly to that characterizing the anterior-posterior axis in vertebrates or arthropods.

prdl-a, a gene marker for hydra apical differentiation related to triploblastic paired-like head-specific genes

Two homeobox genes, prdl-a and prdl-b, which were isolated from a Hydra vulgaris cDNA library, encode paired-like class homeodomains highly related to that of the aristaless-related genes. In adult polyps, prdl-b is a marker for synchronously dividing nematoblasts while prdl-a displays an expression restricted to the the nerve cell lineage of the head region. During budding and apical regeneration, an early and transient prdl-a expression was observed in endodermal cells of the stump at a time when the head organizer is established. When apical regeneration was delayed upon concomittant budding, prdl-a expression was found to be altered in the stump. Furthermore, a specific anti-prdl-a protein immunoserum revealed that prdl-a was overexpressed in adult polyps of the Chlorohydra viridissima multiheaded mutant, with an expression domain extending below the tentacle ring towards the body column. Accordingly, prdl-a DNA-binding activity was enhanced in nuclear extracts from this mutant. These results suggest that prdl-a responds to apical forming signals and might thus be involved in apical specification. When a marine hydrozoan (Podocorynae carnea) was used, the anti-prdl-a antibody showed cross-reactivity with cells located around the oral region, indicating that prdl-a function is shared by other cnidaria. The ancestral role for prdl-a-related genes in the molecular definition of the head (or oral-surrounding region) is discussed.

Isolation of a marker for head-specific cell differentiation in hydra

A cDNA was isolated from Hydra vulgaris coding for a 360 amino acid long polypeptide with no significant similarity to any known protein. In situ hybridization showed that the corresponding transcript is expressed exclusively in endodermal cells of the hypostome, hence its name hyp 1. Hyp 1 therefore represents a highly specific marker for the head region of hydra. In accordance with this, we found that hyp 1 expression was strong in tissues regenerating a head. Hyp 1 reappeared early during head regeneration, namely 6-8 h after initiation of regeneration by cutting. These findings imply that hyp 1 is an excellent marker for monitoring early events in head-specific differentiation processes in hydra.

The cAMP response element binding protein is involved in hydra regeneration

Hydra provides an interesting developmental model system where pattern formation processes are easily accessible to experimentation during regeneration. Previous studies have shown that the neuropeptide head activator affects cellular growth and head-specific cellular differentiation during head regeneration and budding. In order to investigate the signal transduction pathway and the regulatory genes involved in these processes, we measured cAMP levels after head activator treatment and found that head activator leads to an increase in cAMP levels at concentrations where effects on nerve cell determination and differentiation are observed (10(−11) to 10(−9) M). Moreover, exposure of intact hydra to a permeable form of cAMP stimulates nerve-cell differentiation and thus mimicks the effect of endogenous head activator. Band-shift assays were performed to detect changes in hydra nuclear protein binding activity during regeneration or after head activator treatment. We found that the cAMP response element (CRE) promotes a specific and strong DNA-binding activity which is dramatically enhanced and modified during early regeneration or after HA treatment. We also identified a surprisingly highly conserved hydra gene encoding the cAMP Response Element Binding protein, which is involved in this CRE-binding activity. Initiation of regeneration upon wounding provokes an endogenous release of HA which leads to the final differentiation of determined nerve cells. We propose that the nerve-cell differentiation observed within the first 4–8 hours of regeneration relies on the agonist effect of head activator on the cAMP pathway, which would in turn modulate the CRE-binding activity of the hydra CREB protein and thus regulate the transcriptional activity of genes involved in regeneration processes.