Evolutionary biology: animal roots and shoots

The first mollusk spätzle homolog gene in the clam, Paphia undulate

Spätzle, is the only identified endogenous Toll receptor ligand, plays a critical role in initiatinge innate immune responses and controlling dorsal-ventral axis formation in Drosophila. Here we identified the first spätzle gene homolog, Pu-Spz, in the marine mollusk Paphia undulate. The full-length of Pu-Spz cDNA is 1248 bp, including an open reading frame (ORF) of 702 bp, a 5'-untranslated region (UTR) of 26 bp and a 3'-UTR of 203 bp. The ORF encodes a 233-amino-acid protein with conserved domains; it includes a putative signal peptide and a C-terminal cystine-knot. Sequence alignment revealed that the cystine-knot domain of Pu-Spz contains six highly conserved Cys residues, which maintain a molecular conformation suitable for Toll receptor binding. Unlike Spätzle, Pu-Spz lacks a seventh Cys residue, which is essential for forming intermolecular disulfide bridge. Phylogenetic analysis revealed that Pu-Spz is closer to the homologs found in crustaceans than to those in the insect branch. Transcript abundance of Pu-Spz was increased after challenging P. undulate with either heat-killed Listeria monocytogenes or heat-killed Vibrio alginolyticus, suggesting Spätzle is involved in P. undulate host defense. Our results demonstrate convergent evolution of the spätzle-Toll system between the mollusk and arthropod lineages.

Metabolites and metals in Metazoa--what role do phytochelatins play in animals?

Phytochelatins are sulfur-rich metal-binding peptides, and phytochelatin synthesis is one of the key mechanisms by which plants protect themselves against toxic soft metal ions such as cadmium. It has been known for a while now that some invertebrates also possess functional phytochelatin synthase (PCS) enzymes, and that at least one species, the nematode Caenorhabditis elegans, produces phytochelatins to help detoxify cadmium, and probably also other metal and metalloid ions including arsenic, zinc, selenium, silver, and copper. Here, we review recent studies on the occurrence, utilization, and regulation of phytochelatin synthesis in invertebrates. The phytochelatin synthase gene has a wide phylogenetic distribution, and can be found in species that cover almost all of the animal tree of life. The evidence to date, though, suggests that the occurrence is patchy, and even though some members of particular taxonomic groups may contain PCS genes, there are also many species without these genes. For animal species that do possess PCS genes, some of them (e.g. earthworms) do synthesize phytochelatins in response to potentially toxic elements, whereas others (e.g. Schistosoma mansoni, a parasitic helminth) do not appear to do so. Just how (and if) phytochelatins in invertebrates complement the function of metallothioneins remains to be elucidated, and the temporal, spatial, and metal specificity of the two systems is still unknown.

Identification and functional characterization of SIMPL in Crassostrea gigas reveals its ancient origin and involvement in the regulation of Rel/NF-κB transcription activity

SIMPL (Signaling Molecule that associates with the mouse Pelle-Like Kinase) has been recently identified as a co-regulator of NF-κB dependent transcription. Here, we report the discovery and functional analysis of the SIMPL in a mollusk, Crassostrea gigas, which terms as CgSIMPL. CgSIMPL is comprised of 252 amino acids and shares significant homology with vertebrate homologs. Over-expression of CgSIMPL does not activate the NF-κB reporter in the HEK293 cell line, but can enhance Rel-dependent NF-κB transactivation. The dominant-negative effect of CgSIMPL was observed after the deletion of NLS, strongly suggesting that NLS is required for the enhancement of Rel-dependent NF-κB transactivation. Furthermore, CgSIMPL mRNA is constitutively expressed in various tissues and is inducible at late stages of infection, supporting its regulatory function in innate immunity. Altogether, our studies reveal that SIMPL is reserved and co-evolved with NF-κB in chordate and mollusk, supporting its ancient origin and involvement in regulation of NF-κB signaling pathway.

Genome-wide identification of novel microRNAs and their target genes in the human parasite Schistosoma mansoni

Mature microRNAs (miRNAs) are small, non-coding regulatory RNAs which can elicit post-transcriptional repression of mRNA levels of target genes. Here, we report the identification of 67 mature and 42 precursor miRNAs in the Schistosoma mansoni parasite. The evolutionarily conserved S. mansoni miRNAs consisted of 26 precursor miRNAs and 35 mature miRNAs, while we identified 16 precursor miRNAs and 32 mature miRNAs that displayed no conservation. These S. mansoni miRNAs are located on seven autosomal chromosomes and a sex (W) chromosome. miRNA expansion through gene duplication was suggested for at least two miRNA families miR-71 and mir-2. miRNA target finding analysis identified 389 predicted mRNA targets for the identified miRNAs and suggests that the sma-mir-71 may be involved in female sexual maturation. Given the important roles of miRNAs in animals, the identification and characterization of miRNAs in S. mansoni will facilitate novel approaches towards prevention and treatment of Schistosomiasis.

Earthworm genomes, genes and proteins: the (re)discovery of Darwin's worms

Small incremental biological change, winnowed by natural selection over geological time scales to produce large consequences, was Darwin's singular insight that revolutionized the life sciences. His publications after 1859, including the ‘earthworm book’, were all written to amplify and support the evolutionary theory presented in the Origin. Darwin was unable to provide a physical basis for the inheritance of favoured traits because of the absence of genetic knowledge that much later led to the ‘modern synthesis’. Mistaken though he was in advocating systemic ‘gemmules’ as agents of inheritance, Darwin was perceptive in seeking to underpin his core vision with concrete factors that both determine the nature of a trait in one generation and convey it to subsequent generations. This brief review evaluates the molecular genetic literature on earthworms published during the last decade, and casts light on the specific aspects of earthworm evolutionary biology that more or less engaged Darwin: (i) biogeography, (ii) species diversity, (iii) local adaptations and (iv) sensitivity. We predict that the current understanding will deepen with the announcement of a draft earthworm genome in Darwin's bicentenary year, 2009. Subsequently, the earthworm may be elevated from the status of a soil sentinel to that elusive entity, an ecologically relevant genetic model organism.

cDNA cloning and expression analysis of Eisenia fetida (Annelida: Oligochaeta) phytochelatin synthase under cadmium exposure

Metallothioneins (MTs) are central to trace metal homeostasis and detoxification throughout biological systems. Prokaryotes, plants, and fungi utilize both gene encoded cysteine-rich polypeptides (classically designated Class I and II MTs) and enzymatically synthesized cysteine-rich peptides (classically designated Class III MTs or phytochelatins). In contrast, although gene encoded MTs are ubiquitous in animal species the identification of a functional phytochelatin synthase in the nematode Caenorhabditis elegans, a representative member of the Ecdysozoa, provided the first evidence for these metal-binding peptides in animals. By exploiting the conservation observed between species we have been able to clone and transcriptionally characterize a phytochelatin synthase from the immune cells of the earthworm Eisenia fetida, the first evidence for its presence in a phylum belonging to the Lophototrochozoa. The complete coding sequence of this enzyme was determined and the phylogenetic relationship to plant, yeast and nematode enzymes elucidated. Temporal- and dose-profiling of the transcriptional regulation of phytochelatin synthase and MT in response to cadmium was performed by using real-time PCR.

The global landscape of sequence diversity

BACKGROUND

Systematic comparisons between genomic sequence datasets have revealed a wide spectrum of sequence specificity from sequences that are highly conserved to those that are specific to individual species. Due to the limited number of fully sequenced eukaryotic genomes, analyses of this spectrum have largely focused on prokaryotes. Combining existing genomic datasets with the partial genomes of 193 eukaryotes derived from collections of expressed sequence tags, we performed a quantitative analysis of the sequence specificity spectrum to provide a global view of the origins and extent of sequence diversity across the three domains of life.

RESULTS

Comparisons with prokaryotic datasets reveal a greater genetic diversity within eukaryotes that may be related to differences in modes of genetic inheritance. Mapping this diversity within a phylogenetic framework revealed that the majority of sequences are either highly conserved or specific to the species or taxon from which they derive. Between these two extremes, several evolutionary landmarks consisting of large numbers of sequences conserved within specific taxonomic groups were identified. For example, 8% of sequences derived from metazoan species are specific and conserved within the metazoan lineage. Many of these sequences likely mediate metazoan specific functions, such as cell-cell communication and differentiation.

CONCLUSION

Through the use of partial genome datasets, this study provides a unique perspective of sequence conservation across the three domains of life. The provision of taxon restricted sequences should prove valuable for future computational and biochemical analyses aimed at understanding evolutionary and functional relationships.

The emergence and loss of gonadotropin-releasing hormone in protostomes: orthology, phylogeny, structure, and function

Gonadotropin-releasing hormone (GNRH) is a neuropeptide critical for reproductive activation and maintenance in vertebrates. The recent elucidation of molluscan GNRH-like sequences led to several important questions regarding the evolution of the GNRH family. For instance, are molluscan and chordate GNRHs true orthologs? Has GNRH been retained in most protostomian lineages? What was the function of the ancestral GNRH? The goal of this review is to provide a critical analysis of GNRH evolution based on data available from the known forms of protostomian GNRH. Judging from the orthology between chordate and protostomian GNRH receptors, conservation of several structural motifs on the GNRH peptide, and exon/intron arrangement conserved between protostomian and chordate GNRH genomic sequences, we conclude that chordate and protostomian GNRHs likely share a common ancestor. Based on our analysis of phylogenetic distribution, we also hypothesize that GNRH may have been lost in the ecdysozoan lineage but preserved in lophotrochozoans. Lastly, we propose that the ancestral function of GNRH is to serve as a general neural regulator, and its considerable specialization in reproduction seen in chordates is a consequence of neofunctionalization following gene duplication.

Transcriptome profiling of developmental and xenobiotic responses in a keystone soil animal, the oligochaete annelid Lumbricus rubellus

Background

Natural contamination and anthropogenic pollution of soils are likely to be major determinants of functioning and survival of keystone invertebrate taxa. Soil animals will have both evolutionary adaptation and genetically programmed responses to these toxic chemicals, but mechanistic understanding of such is sparse. The clitellate annelid Lumbricus rubellus is a model organism for soil health testing, but genetic data have been lacking.

Results

We generated a 17,000 sequence expressed sequence tag dataset, defining ~8,100 different putative genes, and built an 8,000-element transcriptome microarray for L. rubellus. Strikingly, less than half the putative genes (43%) were assigned annotations from the gene ontology (GO) system; this reflects the phylogenetic uniqueness of earthworms compared to the well-annotated model animals. The microarray was used to identify adult- and juvenile-specific transcript profiles in untreated animals and to determine dose-response transcription profiles following exposure to three xenobiotics from different chemical classes: inorganic (the metal cadmium), organic (the polycyclic aromatic hydrocarbon fluoranthene), and agrochemical (the herbicide atrazine). Analysis of these profiles revealed compound-specific fingerprints which identify the molecular responses of this annelid to each contaminant. The data and analyses are available in an integrated database, LumbriBASE.

Conclusion

L. rubellus has a complex response to contaminant exposure, but this can be efficiently analysed using molecular methods, revealing unique response profiles for different classes of effector. These profiles may assist in the development of novel monitoring or bioremediation protocols, as well as in understanding the ecosystem effects of exposure.

Analysis of Schistosoma mansoni genes shared with Deuterostomia and with possible roles in host interactions

BACKGROUND

Schistosoma mansoni is a blood helminth parasite that causes schistosomiasis, a disease that affects 200 million people in the world. Many orthologs of known mammalian genes have been discovered in this parasite and evidence is accumulating that some of these genes encode proteins linked to signaling pathways in the parasite that appear to be involved with growth or development, suggesting a complex co-evolutionary process.

RESULTS

In this work we found 427 genes conserved in the Deuterostomia group that have orthologs in S. mansoni and no members in any nematodes and insects so far sequenced. Among these genes we have identified Insulin Induced Gene (INSIG), Interferon Regulatory Factor (IRF) and vasohibin orthologs, known to be involved in mammals in mevalonate metabolism, immune response and angiogenesis control, respectively. We have chosen these three genes for a more detailed characterization, which included extension of their cloned messages to obtain full-length sequences. Interestingly, SmINSIG showed a 10-fold higher expression in adult females as opposed to males, in accordance with its possible role in regulating egg production. SmIRF has a DNA binding domain, a tryptophan-rich N-terminal region and several predicted phosphorylation sites, usually important for IRF activity. Fourteen different alternatively spliced forms of the S. mansoni vasohibin (SmVASL) gene were detected that encode seven different protein isoforms including one with a complete C-terminal end, and other isoforms with shorter C-terminal portions. Using S. mansoni homologs, we have employed a parsimonious rationale to compute the total gene losses/gains in nematodes, arthropods and deuterostomes under either the Coelomata or the Ecdysozoa evolutionary hypotheses; our results show a lower losses/gains number under the latter hypothesis.

CONCLUSION

The genes discussed which are conserved between S. mansoni and deuterostomes, probably have an ancient origin and were lost in Ecdysozoa, being still present in Lophotrochozoa. Given their known functions in Deuterostomia, it is possible that some of them have been co-opted to perform functions related (directly or indirectly) to host adaptation or interaction with host signaling processes.

Support for the Coelomata clade of animals from a rigorous analysis of the pattern of intron conservation

Many intron positions are conserved in varying subsets of eukaryotic genomes and, consequently, comprise a potentially informative class of phylogenetic characters. Roy and Gilbert developed a method of phylogenetic reconstruction using the patterns of intron presence-absence in eukaryotic genes and, applying this method to the analysis of animal phylogeny, obtained support for an Ecdysozoa clade (Roy SW, Gilbert W. 2005. Resolution of a deep animal divergence by the pattern of intron conservation. Proc Natl Acad Sci USA. 102:4403-4408). The critical assumption in the method was the independence of intron loss in different branches of the phylogenetic tree. Here, this assumption is refuted by showing that the branch-specific intron loss rates are strongly correlated. We show that different tree topologies are obtained, in each case with a significant statistical support, when different subsets of intron positions are analyzed. The analysis of the conserved intron positions supports the Coelomata topology, that is, a clade comprised of arthropods and chordates, whereas the analysis of more variable intron positions favors the Ecdysozoa topology, that is, a clade of arthropods and nematodes. We show, however, that the support for Ecdysozoa is fully explained by parallel loss of introns in nematodes and arthropods, a factor that does not contribute to the analysis of the conserved introns. The developed procedure for the identification and analysis of conserved introns and other characters with minimal or no homoplasy is expected to be useful for resolving many hard phylogenetic problems.

Phylogenomics of caspase-activated DNA fragmentation factor

The degradation of nuclear DNA by DNA fragmentation factor (DFF) is a key step in apoptosis of mammalian cells. Using comparative genomics, we have here determined the evolutionary history of the genes encoding the two DFF subunits, DFFA (also known as ICAD) and DFFB (CAD). Orthologs of DFFA and DFFB were identified in Nematostella vectensis, a representative of the primitive metazoan clade cnidarians, and in various vertebrates and insects, but not in representatives of urochordates, echinoderms, and nematodes. The domains mediating the interaction of DFFA and DFFB, a caspase cleavage site in DFFA, and the amino acid residues critical for endonuclease activity of DFFB were conserved in Nematostella. These findings suggest that DFF has been a part of the primordial apoptosis system of the eumetazoan common ancestor and that the ancient cell death machinery has degenerated in several evolutionary lineages, including the one leading to the prototypical apoptosis model, Caenorhabditis elegans.

Characterization of a Rel\NF-kappaB homologue in a gastropod abalone, Haliotis diversicolor supertexta

Rel\NF-kappaB signal transduction pathway is evolutionarily conserved and involved in numerous biological processes. We report here, for the first time that a homologue of Rel\NF-kappaB transcription factor, Ab-Rel, was identified and functionally characterized in a gastropod abalone, H. diversicolor supertexta. The full-length Ab-Rel cDNA consists of 1943 bp with an ORF encoding a 584 amino acids protein. Amino acid sequence analysis revealed that Ab-Rel shares conserved signature motifs with other Rel proteins, including the Rel homology domain (RHD), nuclear localization signal (NLS) and phosphorylation site, RRPS. Northern hybridization and real-time PCR indicated that Ab-Rel was ubiquitously and constitutively expressed in abalone. The recombinant Ab-Rel RHD protein was confirmed to specifically bind the consensus NF-kappaB binding site. Furthermore, EMSA showed that NF-kappaB activity was induced in abalone hemocytes by stimulation with LPS. These results strongly suggest that Ab-Rel is a Rel homologue, which plays a conserved role in the immune response of the ancient invertebrate, abalone, allowing us to study the Rel\NF-kappaB signaling pathway in an evolutionary context.

Human and environmental risk assessment of pharmaceuticals: differences, similarities, lessons from toxicology

The presence of human and veterinary pharmaceuticals in the environment has caused increasing concern due their effects on ecological receptors. Improving the risk assessment of these compounds necessitates a quantitative understanding of their metabolism and elimination in the target organism (toxicokinetics), particularly via the ubiquitous cytochrome P-450 (CYP) system and their mechanisms of toxicity (toxicodynamics). This review focuses on a number of pharmaceuticals and veterinary medicines of environmental concern, and the differences and similarities between ecological and human risk assessment. CYP metabolism is discussed with particular reference to its ubiquity in species of ecological relevance. The important issue of pharmaceutical mixtures is discussed to assess how emerging technologies such as ecotoxicogenomics may assist in moving towards a more mechanism-based environmental risk assessment of pharmaceuticals.