Changing hydrozoan bauplans by silencing Hox-like genes

Gene Loss may have Shaped the Cnidarian and Bilaterian Hox and ParaHox Complement

Hox and ParaHox transcription factors are important for specifying cell fates along the primary body axes during the development of most animals. Within Cnidaria, much of the research on Hox/ParaHox genes has focused on Anthozoa (anemones and corals) and Hydrozoa (hydroids) and has concentrated on the evolution and function of cnidarian Hox genes in relation to their bilaterian counterparts. Here we analyze together the full complement of Hox and ParaHox genes from species representing all four medusozoan classes (Staurozoa, Cubozoa, Hydrozoa, and Scyphozoa) and both anthozoan classes (Octocorallia and Hexacorallia). Our results show that Hox genes involved in patterning the directive axes of anthozoan polyps are absent in the stem leading to Medusozoa. For the first time, we show spatial and temporal expression patterns of Hox and ParaHox genes in the upside-down jellyfish Cassiopea xamachana (Scyphozoa), which are consistent with diversification of medusozoan Hox genes both from anthozoans and within medusozoa. Despite unprecedented taxon sampling, our phylogenetic analyses, like previous studies, are characterized by a lack of clear homology between most cnidarian and bilaterian Hox and Hox-related genes. Unlike previous studies, we propose the hypothesis that the cnidarian-bilaterian ancestor possessed a remarkably large Hox complement and that extensive loss of Hox genes was experienced by both cnidarian and bilaterian lineages.

Renewed perspectives on the sedentary-pelagic last common bilaterian ancestor

Various evaluations of the last common bilaterian ancestor (lcba) currently suggest that it resembled either a microscopic, non-segmented motile adult; or, on the contrary, a complex segmented adult motile urbilaterian. These fundamental inconsistencies remain largely unexplained. A majority of multidisciplinary data regarding sedentary adult ancestral bilaterian organization is overlooked. The sedentary-pelagic model is supported now by a number of novel developmental, paleontological and molecular phylogenetic data: (1) data in support of sedentary sponges, in the adult stage, as sister to all other Metazoa; (2) a similarity of molecular developmental pathways in both adults and larvae across sedentary sponges, cnidarians, and bilaterians; (3) a cnidarian-bilaterian relationship, including a unique sharing of a bona fide Hox-gene cluster, of which the evolutionary appearance does not connect directly to a bilaterian motile organization; (4) the presence of sedentary and tube-dwelling representatives of the main bilaterian clades in the early Cambrian; (5) an absence of definite taxonomic attribution of Ediacaran taxa reconstructed as motile to any true bilaterian phyla; (6) a similarity of tube morphology (and the clear presence of a protoconch-like apical structure of the Ediacaran sedentary Cloudinidae) among shells of the early Cambrian, and later true bilaterians, such as semi-sedentary hyoliths and motile molluscs; (7) recent data that provide growing evidence for a complex urbilaterian, despite a continuous molecular phylogenetic controversy. The present review compares the main existing models and reconciles the sedentary model of an urbilaterian and the model of a larva-like lcba with a unified sedentary(adult)-pelagic(larva) model of the lcba.

Hox and Wnt pattern the primary body axis of an anthozoan cnidarian before gastrulation

Hox gene transcription factors are important regulators of positional identity along the anterior–posterior axis in bilaterian animals. Cnidarians (e.g., sea anemones, corals, and hydroids) are the sister group to the Bilateria and possess genes related to both anterior and central/posterior class Hox genes. Here we report a previously unrecognized domain of Hox expression in the starlet sea anemone, Nematostella vectensis, beginning at early blastula stages. We explore the relationship of two opposing Hox genes (NvAx6/NvAx1) expressed on each side of the blastula during early development. Functional perturbation reveals that NvAx6 and NvAx1 not only regulate their respective expression domains, but also interact with Wnt genes to pattern the entire oral–aboral axis. These findings suggest an ancient link between Hox/Wnt patterning during axis formation and indicate that oral–aboral domains are likely established during blastula formation in anthozoan cnidarians.

Hox genes regulate anterior–posterior axis formation but their role in cnidarians is unclear. Here, the authors disrupt Hox genes NvAx1 and NvAx6 in the starlet sea anemone, Nematostella vectensis, showing antagonist function in patterning the oral–aboral axis and a link to Wnt signaling.

Interspecific Differential Expression Analysis of RNA-Seq Data Yields Insight into Life Cycle Variation in Hydractiniid Hydrozoans

Hydrozoans are known for their complex life cycles, which can alternate between an asexually reproducing polyp stage and a sexually reproducing medusa stage. Most hydrozoan species, however, lack a free-living medusa stage and instead display a developmentally truncated form, called a medusoid or sporosac, which generally remains attached to the polyp. Although evolutionary transitions in medusa truncation and loss have been investigated phylogenetically, little is known about the genes involved in the development and loss of this life cycle stage. Here, we present a new workflow for evaluating differential expression (DE) between two species using short read Illumina RNA-seq data. Through interspecific DE analyses between two hydractiniid hydrozoans, Hydractinia symbiolongicarpus and Podocoryna carnea, we identified genes potentially involved in the developmental, functional, and morphological differences between the fully developed medusa of P. carnea and reduced sporosac of H. symbiolongicarpus. A total of 10,909 putative orthologs of H. symbiolongicarpus and P. carnea were identified from de novo assemblies of short read Illumina data. DE analysis revealed 938 of these are differentially expressed between P. carnea developing and adult medusa, when compared with H. symbiolongicarpus sporosacs, the majority of which have not been previously characterized in cnidarians. In addition, several genes with no corresponding ortholog in H. symbiolongicarpus were expressed in developing medusa of P. carnea. Results presented here show interspecific DE analyses of RNA-seq data to be a sensitive and reliable method for identifying genes and gene pathways potentially involved in morphological and life cycle differences between species.

Novel matrix proteins of Pteria penguin pearl oyster shell nacre homologous to the jacalin-related β-prism fold lectins

Nacreous layers of pearl oyster are one of the major functional biominerals. By participating in organic compound-crystal interactions, they assemble into consecutive mineral lamellae-like photonic crystals. Their biomineralization mechanisms are controlled by macromolecules; however, they are largely unknown. Here, we report two novel lectins termed PPL2A and PPL2B, which were isolated from the mantle and the secreted fluid of Pteria penguin oyster. PPL2A is a hetero-dimer composed of α and γ subunits, and PPL2B is a homo-dimer of β subunit, all of which surprisingly shared sequence homology with the jacalin-related plant lectin. On the basis of knockdown experiments at the larval stage, the identification of PPLs in the shell matrix, and in vitro CaCO₃ crystallization analysis, we conclude that two novel jacalin-related lectins participate in the biomineralization of P. penguin nacre as matrix proteins. Furthermore, it was found that trehalose, which is specific recognizing carbohydrates for PPL2A and is abundant in the secreted fluid of P. penguin mantle, functions as a regulatory factor for biomineralization via PPL2A. These observations highlight the unique functions, diversity and molecular evolution of this lectin family involved in the mollusk shell formation.

Molecular insights into the origin of the Hox-TALE patterning system

Despite tremendous body form diversity in nature, bilaterian animals share common sets of developmental genes that display conserved expression patterns in the embryo. Among them are the Hox genes, which define different identities along the anterior–posterior axis. Hox proteins exert their function by interaction with TALE transcription factors. Hox and TALE members are also present in some but not all non-bilaterian phyla, raising the question of how Hox–TALE interactions evolved to provide positional information. By using proteins from unicellular and multicellular lineages, we showed that these networks emerged from an ancestral generic motif present in Hox and other related protein families. Interestingly, Hox-TALE networks experienced additional and extensive molecular innovations that were likely crucial for differentiating Hox functions along body plans. Together our results highlight how homeobox gene families evolved during eukaryote evolution to eventually constitute a major patterning system in Eumetazoans.

DOI:http://dx.doi.org/10.7554/eLife.01939.001

Any animal with a body that is symmetric about an imaginary line that runs from its head to its tail is known as a bilaterian. Humans and most animals are bilateral, whereas jellyfish and starfish are not. Bilateral symmetry can take many forms—as demonstrated by the differences between flies, frogs and humans—but all bilaterians express many of the same genes during development.

One of these groups of genes is known as the Hox family. The expression of specific Hox genes at specific times instructs cells in the developing embryo to adopt different fates according to their position along the anterior–posterior (head to tail) axis. The patterning function of Hox genes relies on the presence of two additional cofactors that belong to the so-called TALE family. Although both Hox and TALE proteins were present early on during animal evolution, it is unclear how and when the interactions between them first began to generate symmetrical body plans.

Now, Hudry et al. have provided insights into the origin of the Hox-TALE network by analysing the expression and molecular properties of Hox and TALE proteins from various multicellular and unicellular organisms. These experiments revealed that Hox and TALE proteins of the sea anemone Nematostella, which belongs to a group of animals called cnidarians that have radial rather than bilateral symmetry, interact with one another in a similar manner to the interactions seen in bilaterians.

Hudry et al. then showed that two Nematostella Hox genes were able to substitute for their bilaterian equivalents in fruit flies, and that a Nematostella TALE gene was able to take over neuronal functions of its equivalent in Xenopus frogs. This striking conservation of function between species suggests that Hox and TALE genes were already working together in the common ancestor of all bilaterian and cnidarian animals.

By contrast, TALE members from a unicellular amoeba were unable to interact with Hox proteins, suggesting that Hox–TALE interactions first emerged in multicellular animals. In addition to increasing our knowledge of highly conserved Hox signalling, these data provide insight into the molecular mechanisms that gave rise to the symmetrical body plan that has been adopted, and adapted, by the majority of animals since.

DOI:http://dx.doi.org/10.7554/eLife.01939.002

Coral comparative genomics reveal expanded Hox cluster in the cnidarian-bilaterian ancestor

The key developmental role of the Hox cluster of genes was established prior to the last common ancestor of protostomes and deuterostomes and the subsequent evolution of this cluster has played a major role in the morphological diversity exhibited in extant bilaterians. Despite 20 years of research into cnidarian Hox genes, the nature of the cnidarian-bilaterian ancestral Hox cluster remains unclear. In an attempt to further elucidate this critical phylogenetic node, we have characterized the Hox cluster of the recently sequenced Acropora digitifera genome. The A. digitifera genome contains two anterior Hox genes (PG1 and PG2) linked to an Eve homeobox gene and an Anthox1A gene, which is thought to be either a posterior or posterior/central Hox gene. These data show that the Hox cluster of the cnidarian-bilaterian ancestor was more extensive than previously thought. The results are congruent with the existence of an ancient set of constraints on the Hox cluster and reinforce the importance of incorporating a wide range of animal species to reconstruct critical ancestral nodes.

Comparative molecular developmental aspects of the mammalian- and the avian lungs, and the insectan tracheal system by branching morphogenesis: recent advances and future directions

Gas exchangers fundamentally form by branching morphogenesis (BM), a mechanistically profoundly complex process which derives from coherent expression and regulation of multiple genes that direct cell-to-cell interactions, differentiation, and movements by signaling of various molecular morphogenetic cues at specific times and particular places in the developing organ. Coordinated expression of growth-instructing factors determines sizes and sites where bifurcation occurs, by how much a part elongates before it divides, and the angle at which branching occurs. BM is essentially induced by dualities of factors where through feedback- or feed forward loops agonists/antagonists are activated or repressed. The intricate transactions between the development orchestrating molecular factors determine the ultimate phenotype. From the primeval time when the transformation of unicellular organisms to multicellular ones occurred by systematic accretion of cells, BM has been perpetually conserved. Canonical signalling, transcriptional pathways, and other instructive molecular factors are commonly employed within and across species, tissues, and stages of development. While much still remain to be elucidated and some of what has been reported corroborated and reconciled with rest of existing data, notable progress has in recent times been made in understanding the mechanism of BM. By identifying and characterizing the morphogenetic drivers, and markers and their regulatory dynamics, the elemental underpinnings of BM have been more precisely explained. Broadening these insights will allow more effective diagnostic and therapeutic interventions of developmental abnormalities and pathologies in pre- and postnatal lungs. Conservation of the molecular factors which are involved in the development of the lung (and other branched organs) is a classic example of nature's astuteness in economically utilizing finite resources. Once purposefully formed, well-tested and tried ways and means are adopted, preserved, and widely used to engineer the most optimal phenotypes. The material and time costs of developing utterly new instruments and routines with every drastic biological change (e.g. adaptation and speciation) are circumvented. This should assure the best possible structures and therefore functions, ensuring survival and evolutionary success.

Isolation of Hox cluster genes from insects reveals an accelerated sequence evolution rate

Among gene families it is the Hox genes and among metazoan animals it is the insects (Hexapoda) that have attracted particular attention for studying the evolution of development. Surprisingly though, no Hox genes have been isolated from 26 out of 35 insect orders yet, and the existing sequences derive mainly from only two orders (61% from Hymenoptera and 22% from Diptera). We have designed insect specific primers and isolated 37 new partial homeobox sequences of Hox cluster genes (lab, pb, Hox3, ftz, Antp, Scr, abd-a, Abd-B, Dfd, and Ubx) from six insect orders, which are crucial to insect phylogenetics. These new gene sequences provide a first step towards comparative Hox gene studies in insects. Furthermore, comparative distance analyses of homeobox sequences reveal a correlation between gene divergence rate and species radiation success with insects showing the highest rate of homeobox sequence evolution.

The origin of patterning systems in bilateria-insights from the Hox and ParaHox genes in Acoelomorpha

Hox and ParaHox genes constitute two families of developmental regulators that pattern the Anterior–Posterior body axis in all bilaterians. The members of these two groups of genes are usually arranged in genomic clusters and work in a coordinated fashion, both in space and in time. While the mechanistic aspects of their action are relatively well known, it is still unclear how these systems evolved. For instance, we still need a proper model of how the Hox and ParaHox clusters were assembled over time. This problem is due to the shortage of information on gene complements for many taxa (mainly basal metazoans) and the lack of a consensus phylogenetic model of animal relationships to which we can relate our new findings. Recently, several studies have shown that the Acoelomorpha most probably represent the first offshoot of the Bilateria. This finding has prompted us, and others, to study the Hox and ParaHox complements in these animals, as well as their activity during development. In this review, we analyze how the current knowledge of Hox and ParaHox genes in the Acoelomorpha is shaping our view of bilaterian evolution.

RNA interference in marine and freshwater sponges: actin knockdown in Tethya wilhelma and Ephydatia muelleri by ingested dsRNA expressing bacteria

Background

The marine sponge Tethya wilhelma and the freshwater sponge Ephydatia muelleri are emerging model organisms to study evolution, gene regulation, development, and physiology in non-bilaterian animal systems. Thus far, functional methods (i.e., loss or gain of function) for these organisms have not been available.

Results

We show that soaking developing freshwater sponges in double-stranded RNA and/or feeding marine and freshwater sponges bacteria expressing double-stranded RNA can lead to RNA interference and reduction of targeted transcript levels. These methods, first utilized in C. elegans, have been adapted for the development and feeding style of easily cultured marine and freshwater poriferans. We demonstrate phenotypic changes result from 'knocking down' expression of the actin gene.

Conclusion

This technique provides an easy, efficient loss-of-function manipulation for developmental and gene regulatory studies in these important non-bilaterian animals.

Dicer functions in aquatic species

Dicer is an RNase III enzyme with two catalytic subunits, which catalyzes the cleavage of double-stranded RNA to small interfering RNAs and micro-RNAs, which are mainly involved in invasive nucleic acid defense and endogenous genes regulation. Dicer is abundantly expressed in embryos, indicating the importance of the protein in early embryonic development. In addition, Dicer is thought to be involved in defense mechanism against foreign nucleic acids such as viruses. This paper will mainly focus on the recent progress of Dicer-related research and discuss potential RNA interference pathways in aquatic species.

Exposure to dsRNA elicits RNA interference in Brachionus manjavacas (Rotifera)

RNA interference (RNAi) is a powerful technique for functional genomics, yet no studies have reported its successful application to zooplankton. Many zooplankton, particularly microscopic metazoans of phylum Rotifera, have unique life history traits for which genetic investigation has been limited. In this paper, we report the development of RNAi methods for rotifers, with the exogenous introduction of double-stranded RNA (dsRNA) through the use of a lipofection reagent. Transfection with dsRNA for heat shock protein 90, the membrane-associated progesterone receptor, and mitogen-activated protein kinase significantly increased the proportion of non-reproductive females. Additionally, a fluorescence-based lectin binding assay confirmed the significant suppression of four of six glycosylation enzymes that were targeted with dsRNA. Suppression of mRNA transcripts was confirmed with quantitative PCR. Development of RNAi for rotifers promises to enhance the ability for assessing genetic regulation of features critical to their life history and represents a key step toward functional genomics research in zooplankton.

Evolution of Hox complexes

Recent years have seen a plethora of ideas and hypotheses, and lots of debate, about the origin and evolution of the Hox gene cluster. Here I will attempt to summarize these hypotheses, identify their strengths and weaknesses and highlight the types of new data that may lead to further resolution of the competing ideas. The major theme is that Hox genes originated very early in animal evolution and extensive independent duplications occurred in major lineages. Duplications however have not been the only route to change in the composition and structure of the Hox cluster, as extensive gene losses have occurred as well. Indeed it is gene loss that is one of the main obstacles in our understanding of the origin and evolution of Hox clusters. Matters should be improved with wider taxon sampling along with a clearer understanding of how duplicated genes evolve.

Regulation of Hox activity: insights from protein motifs

Deciphering the molecular bases of animal body plan construction is a central question in developmental and evolutionary biology. Genome analyses of a number of metazoans indicate that widely conserved regulatory molecules underlie the amazing diversity of animal body plans, suggesting that these molecules are reiteratively used for multiple purposes. Hox proteins constitute a good example of such molecules and provide the framework to address the mechanisms underlying transcriptional specificity and diversity in development and evolution. Here we examine the current knowledge of the molecular bases of Hox-mediated transcriptional control, focusing on how this control is encoded within protein sequences and structures. The survey suggests that the homeodomain is part of an extended multifunctional unit coordinating DNA binding and activity regulation and highlights the need for further advances in our understanding of Hox protein activity.

Origins of neurogenesis, a cnidarian view

New perspectives on the origin of neurogenesis emerged with the identification of genes encoding post-synaptic proteins as well as many "neurogenic" regulators as the NK, Six, Pax, bHLH proteins in the Demosponge genome, a species that might differentiate sensory cells but no neurons. However, poriferans seem to miss some key regulators of the neurogenic circuitry as the Hox/paraHox and Otx-like gene families. Moreover as a general feature, many gene families encoding evolutionarily-conserved signaling proteins and transcription factors were submitted to a wave of gene duplication in the last common eumetazoan ancestor, after Porifera divergence. In contrast gene duplications in the last common bilaterian ancestor, Urbilateria, are limited, except for the bHLH Atonal-class. Hence Cnidaria share with Bilateria a large number of genetic tools. The expression and functional analyses currently available suggest a neurogenic function for numerous orthologs in developing or adult cnidarians where neurogenesis takes place continuously. As an example, in the Hydra polyp, the Clytia medusa and the Acropora coral, the Gsx/cnox2/Anthox-2 ParaHox gene likely supports neurogenesis. Also neurons and nematocytes (mechanosensory cells) share in hydrozoans a common stem cell and several regulatory genes indicating that they can be considered as sister cells. Performed in anthozoan and medusozoan species, these studies should tell us more about the way(s) evolution hazards achieved the transition from epithelial to neuronal cell fate, and about the robustness of the genetic circuitry that allowed neuromuscular transmission to arise and be maintained across evolution.

Concatenated analysis sheds light on early metazoan evolution and fuels a modern "urmetazoon" hypothesis

For more than a century, the origin of metazoan animals has been debated. One aspect of this debate has been centered on what the hypothetical “urmetazoon” bauplan might have been. The morphologically most simply organized metazoan animal, the placozoan Trichoplax adhaerens, resembles an intriguing model for one of several “urmetazoon” hypotheses: the placula hypothesis. Clear support for a basal position of Placozoa would aid in resolving several key issues of metazoan-specific inventions (including, for example, head–foot axis, symmetry, and coelom) and would determine a root for unraveling their evolution. Unfortunately, the phylogenetic relationships at the base of Metazoa have been controversial because of conflicting phylogenetic scenarios generated while addressing the question. Here, we analyze the sum of morphological evidence, the secondary structure of mitochondrial ribosomal genes, and molecular sequence data from mitochondrial and nuclear genes that amass over 9,400 phylogenetically informative characters from 24 to 73 taxa. Together with mitochondrial DNA genome structure and sequence analyses and Hox-like gene expression patterns, these data (1) provide evidence that Placozoa are basal relative to all other diploblast phyla and (2) spark a modernized “urmetazoon” hypothesis.

Following one of the basic principles in evolutionary biology that complex life forms derive from more primitive ancestors, it has long been believed that the higher animals, the Bilateria, arose from simpler (diploblastic) organisms such as the cnidarians (corals, polyps, and jellyfishes). A large number of studies, using different datasets and different methods, have tried to determine the most ancestral animal group as well as the ancestor of the higher animals. Here, we use “total evidence” analysis, which incorporates all available data (including morphology, genome, and gene expression data) and come to a surprising conclusion. The Bilateria and Cnidaria (together with the other diploblastic animals) are in fact sister groups: that is, they evolved in parallel from a very simple common ancestor. We conclude that the higher animals (Bilateria) and lower animals (diploblasts), probably separated very early, at the very beginning of metazoan animal evolution and independently evolved their complex body plans, including body axes, nervous system, sensory organs, and other characteristics. The striking similarities in several complex characters (such as the eyes) resulted from both lineages using the same basic genetic tool kit, which was already present in the common ancestor. The study identifies Placozoa as the most basal diploblast group and thus a living fossil genome that nicely demonstrates, not only that complex genetic tool kits arise before morphological complexity, but also that these kits may form similar morphological structures in parallel.

Total evidence analyses reveal a surprise: Higher animals did not evolve from any known lower animal group.

Are Hox genes ancestrally involved in axial patterning? Evidence from the hydrozoan Clytia hemisphaerica (Cnidaria)

BACKGROUND

The early evolution and diversification of Hox-related genes in eumetazoans has been the subject of conflicting hypotheses concerning the evolutionary conservation of their role in axial patterning and the pre-bilaterian origin of the Hox and ParaHox clusters. The diversification of Hox/ParaHox genes clearly predates the origin of bilaterians. However, the existence of a "Hox code" predating the cnidarian-bilaterian ancestor and supporting the deep homology of axes is more controversial. This assumption was mainly based on the interpretation of Hox expression data from the sea anemone, but growing evidence from other cnidarian taxa puts into question this hypothesis.

METHODOLOGY/PRINCIPAL FINDINGS

Hox, ParaHox and Hox-related genes have been investigated here by phylogenetic analysis and in situ hybridisation in Clytia hemisphaerica, an hydrozoan species with medusa and polyp stages alternating in the life cycle. Our phylogenetic analyses do not support an origin of ParaHox and Hox genes by duplication of an ancestral ProtoHox cluster, and reveal a diversification of the cnidarian HOX9-14 genes into three groups called A, B, C. Among the 7 examined genes, only those belonging to the HOX9-14 and the CDX groups exhibit a restricted expression along the oral-aboral axis during development and in the planula larva, while the others are expressed in very specialised areas at the medusa stage.

CONCLUSIONS/SIGNIFICANCE

Cross species comparison reveals a strong variability of gene expression along the oral-aboral axis and during the life cycle among cnidarian lineages. The most parsimonious interpretation is that the Hox code, collinearity and conservative role along the antero-posterior axis are bilaterian innovations.