Shirley A. Pomponi

Reconstruction of Family-Level Phylogenetic Relationships within Demospongiae (Porifera) Using Nuclear Encoded Housekeeping Genes

Background Demosponges are challenging for phylogenetic systematics because of their plastic and relatively simple morphologies and many deep divergences between major clades. To improve understanding of the phylogenetic relationships within Demospongiae, we sequenced and analyzed seven nuclear housekeeping genes involved in a variety of cellular functions from a diverse group of sponges. Methodology/Principal Findings We generated data from each of the four sponge classes (i.e., Calcarea, Demospongiae, Hexactinellida, and Homoscleromorpha), but focused on family-level relationships within demosponges. With data for 21 newly sampled families, our Maximum Likelihood and Bayesian-based approaches recovered previously phylogenetically defined taxa: Keratosap, Myxospongiaep, Spongillidap, Haploscleromorphap (the marine haplosclerids) and Democlaviap. We found conflicting results concerning the relationships of Keratosap and Myxospongiaep to the remaining demosponges, but our results strongly supported a clade of Haploscleromorphap+Spongillidap+Democlaviap. In contrast to hypotheses based on mitochondrial genome and ribosomal data, nuclear housekeeping gene data suggested that freshwater sponges (Spongillidap) are sister to Haploscleromorphap rather than part of Democlaviap. Within Keratosap, we found equivocal results as to the monophyly of Dictyoceratida. Within Myxospongiaep, Chondrosida and Verongida were monophyletic. A well-supported clade within Democlaviap, Tetractinellidap, composed of all sampled members of Astrophorina and Spirophorina (including the only lithistid in our analysis), was consistently revealed as the sister group to all other members of Democlaviap. Within Tetractinellidap, we did not recover monophyletic Astrophorina or Spirophorina. Our results also reaffirmed the monophyly of order Poecilosclerida (excluding Desmacellidae and Raspailiidae), and polyphyly of Hadromerida and Halichondrida. Conclusions/Significance These results, using an independent nuclear gene set, confirmed many hypotheses based on ribosomal and/or mitochondrial genes, and they also identified clades with low statistical support or clades that conflicted with traditional morphological classification. Our results will serve as a basis for future exploration of these outstanding questions using more taxon- and gene-rich datasets.

A chemical view of the most ancient metazoa – biomarker chemotaxonomy of hexactinellid sponges

Hexactinellid sponges are often considered to be the most ancient metazoans. Lipid biomarkers from 23 species were studied for information on their phylogenetic properties, particularly their disputed relation to the two other sponge classes (Demospongiae, Calcarea). The most prominent lipid compounds in the Hexactinellida comprise C28 to C32 polyenoic fatty acids. Their structures parallel the unique patterns found in demosponge membrane fatty acids (demospongic acids) and strongly support a close phylogenetic association of the Demospongiae and the Hexactinellida. Both taxa also show unusual mid-chain methylated fatty acids (C15–C25) and irregular C25- and C40-isoprenoid hydrocarbons, tracers for specific eubacteria and Archaea, respectively. These biomarkers indicate a similar, highly conservative symbiont community, although some shift in the abundance of the associated microbiota was observed. The lack of these features in calcareous sponges further contradicts the still common view that Calcarea and Demospongiae are more closely related to each other than either is to the Hexactinellida.

Cultivation of sponges, sponge cells and symbionts: achievements and future prospects.

Marine sponges are a rich source of bioactive compounds with pharmaceutical potential. Since biological production is one option to supply materials for early drug development, the main challenge is to establish generic techniques for small-scale production of marine organisms. We analysed the state of the art for cultivation of whole sponges, sponge cells and sponge symbionts. To date, cultivation of whole sponges has been most successful in situ; however, optimal conditions are species specific. The establishment of sponge cell lines has been limited by the inability to obtain an axenic inoculum as well as the lack of knowledge on nutritional requirements in vitro. Approaches to overcome these bottlenecks, including transformation of sponge cells and using media based on yolk, are elaborated. Although a number of bioactive metabolite-producing microorganisms have been isolated from sponges, and it has been suggested that the source of most sponge-derived bioactive compounds is microbial symbionts, cultivation of sponge-specific microorganisms has had limited success. The current genomics revolution provides novel approaches to cultivate these microorganisms.

The Early Evolution of the Phosphagen Kinases—Insights from Choanoflagellate and Poriferan Arginine Kinases

Arginine kinase (AK) is a member of a large family of phosphoryl transfer enzymes called phosphagen (guanidino) kinases. AKs are present in certain protozoans, sponges, cnidarians, and both lophotrochozoan and ecdysozoan protostomes. Another phosphagen kinase, creatine kinase (CK), is found in sponges, cnidarians, and both deuterostome and protostome groups but does not appear to be present in protozoans. To probe the early evolution of phosphagen kinases, we have amplified the cDNAs for AKs from three choanoflagellates and from the hexactinellid sponge Aphrocallistes beatrix and the demosponges Suberites fuscus and Microcionaprolifera. Phylogenetic analysis using maximum likelihood of these choanoflagellate and sponge AKs with other AK sequences revealed that the AK from the choanoflagellate Monosiga brevicollis clusters with the AK from the glass sponge Aphrocallistes and is part of a larger cluster containing AKs from the demosponges Suberites and Microciona as well as basal and protostome invertebrates. In contrast, AKs from Codonosiga gracilis and Monosiga ovata form a distinct cluster apart from all other AK sequences. tBLASTn searches of the recently released M. brevicollis genome database showed that this species has three unique AK genes—one virtually identical to the M. brevicollis cDNA and the other two showing great similarity to C. gracilis and M. ovata AKs. Three distinct AK genes are likely present in choanoflagellates. Two of these AKs display extensive similarity to both CKs and an AK from sponges. Previous work has shown CK evolved from an AK-like ancestor prior to the divergence of sponges. The present results provide evidence suggesting that the initial gene duplication event(s) leading to the CK lineage may have occurred before the divergence of the choanoflagellate and animal lineages.

Conservation and phylogeny of a novel family of non-Hox genes of the Antp class in demospongiae (Porifera)

A survey across the most basal animal phylum, the Porifera, for the presence of homeobox-containing genes led to the isolation of 24 partial or complete homeobox sequences from 21 sponge species distributed in 15 families and 6 orders of Demospongiae. All the new sequences shared a high identity/similarity with EmH-3 (Ephydatia muelleri), a non-Hox gene from the Antp class. The Demox sequences, EmH-3, and related homeodomains formed a well-supported clade with no true affinity with any known bilaterian family, including the Tlx/Hox11 family, suggesting that the EmH-3 family of genes, comprising 31 members, represents a novel family of non-Hox genes, called the Demox family, widespread among Demospongiae. The presence of the Tlx/Hox11 specific signature in the Demox family and common regulatory elements suggested that the Demox and Tlx/Hox11 families are closely related. In the phylogenetic analyses, freshwater Haplosclerida appeared as monophyletic, and Haplosclerida and Halichondrida as polyphyletic, with a clade comprising Agelas species and Axinella corrugata. As for their expression, high levels of Demox transcripts were found in adult tissues. Our data add to the number of published poriferan homeobox sequences and provide independent confirmation of the current Demospongiae phylogenies.

Neopetrosiquinones A and B, sesquiterpene benzoquinones isolated from the deep-water sponge Neopetrosia cf. proxima.

Two new marine-derived sesquiterpene benzoquinones which we designate as neopetrosiquinones A (1) and B (2), have been isolated from a deep-water sponge of the family Petrosiidae. The structures were elucidated on the basis of their spectroscopic data. Compounds 1 and 2 inhibit the in vitro proliferation of the DLD-1 human colorectal adenocarcinoma cell line with IC(50) values of 3.7 and 9.8 μM, respectively, and the PANC-1 human pancreatic carcinoma cell line with IC(50) values of 6.1 and 13.8 μM, respectively. Neopetrosiquinone A (1) also inhibited the in vitro proliferation of the AsPC-1 human pancreatic carcinoma cell line with an IC(50) value of 6.1 μM. The compounds are structurally related to alisiaquinone A, cyclozonarone, and xestoquinone.

Cell cycle analysis of primary sponge cell cultures

Proliferation of sponge cells is generally measured via cell counts or viability assays. However, more insight into the proliferative state of a sponge cell population can be obtained from the distribution of the cells over the different phases of the cell cycle. Cell cycle distribution of sponge cells was measured via flow cytometry after staining the DNA with propidium iodide. The five sponges studied in this paper all showed a large fraction of cells in G1/G0 compared to G2/M and S, indicating that cells were not actively dividing. In addition, some sponges also showed a large apoptotic fraction, indicating cell death. Additional apoptosis measurements, based on caspase activity, showed that harvesting and dissociation of sponge tissue to initiate a primary cell culture was directly correlated with an increase in apoptotic cells. This indicates that for the development of cell cultures, more attention should be given to harvesting, dissociation, and quality of starting material. Finally, cultivation conditions used were ineffective for proliferation, since after 2xa0d of cultivating Haliclona oculata cells, most cells shifted towards the apoptotic fraction, indicating that cells were dying. For development of in vitro sponge cell cultures, flow cytometric cell cycle analysis is a useful method to assess the proliferative state of a sponge cell culture and can be used to validate improvements in harvesting and dissociation, to select sponges with good proliferative capacities and to study the influence of culture conditions for stimulating cell growth.

A systematic revision of the Central Atlantic Halichondrida (Demospongiae, Porifera). Part I. Evaluation of characters and diagnosis of the genera

The order Halichondrida has been erected to separate demosponges that possess a confused skeletal arrangement, a simple spicule complement of oxea, and/or styles and a differentiated ectosomal skeleton (Levi 1973; Bergquist 1978; Hartman 1982). Although at present, they are considered a separate order, the problem is recognized of establishing the relationships within the group and with other Demospongiae orders.

First record of the sponge genera Crambe and Discorhabdella for the eastern Pacific, with description of three new species

Three new sponge species are described from the Pacific coast of Panama, namely Crambe panamensis n. sp., Discorhabdella urizae n. sp. and Discorhabdella littoralis n. sp. This is the first record of the genera Crambe and Discorhabdella for the eastern Pacific, which represents not only a considerable expansion in their known biogeographical distribution, but also empirical support for their Tethyan origin. The new species provide a better understanding of the skeletal evolution in these peculiar genera, representing a lineage in which aster-derived spicules occur within a typical poecilosclerid skeleton. The skeleton of C. panamensis consists of ectosomal subtylostyles, choanosomal tylostyles with smooth tyle, basal desmas of astroclone type only, and anchorate isochelae. The skeleton of D. urizae consists of ectosomal subtylostyles, choanosomal tylostyles with tuberose tyle, basal acanthostyles with aster-like tyle, anchorate isochelae, sigmas, and distinctive twisted microxeas. The skeleton of D. littoralis consists of ectosomal tylostyles, choanosomal tylostyles that occasionally show remains of tubercles in the tyle, basal acanthostyles with a tyle intermediate between aster-like and regular morphology, and sigmas. The skeletal affinities of Crambe and Discorhabdella with the genera Lithochela and Monanchora are discussed, and a new family concept based on all four genera is proposed. The name Crambeidae is proposed for such a family, to replace the pre-occupied name Crambidae.

In Vitro Production of Marine-Derived Antitumor Compounds

The sustainable supply of marine-derived bioactive compounds to meet demands for pre-clinical and clinical evaluation is a major consideration in drug development strategies. It is also a concern to environmental resource managers, particularly since conservation of genetic resources may preclude harvesting as a bulk supply strategy. Our research addresses this need by focusing on in vitro production of antitumor compounds through cell culture of the source organisms. Our objectives are: to establish cultures of bioactive marine invertebrates that can be used as models to study in vitro production of antitumor compounds and the factors which control expression of their production; to provide bulk supplies of these compounds through in vitro production; and to produce new structural analogs via manipulation of culture conditions.