The sea urchin genome as a window on function

De Novo Assembly of the Genome of the Sea Urchin Paracentrotus lividus (Lamarck 1816)

The Mediterranean purple sea urchin Paracentrotus lividus (Lamarck 1816) is a remarkable model system for molecular, evolutionary and cell biology studies, particularly in the field of developmental biology. We sequenced the genome, performed a de novo assembly, and analysed the assembly content. The genome of P. lividus was sequenced using Illumina NextSeq 500 System (Illumina) in a 2 × 150 paired-end format. More than 30,000 open reading frames (ORFs), (more than 8000 are unique), were identified and analysed to provide molecular tools accessible for the scientific community. In particular, several genes involved in complex innate immune responses, oxidative metabolism, signal transduction, and kinome, as well as genes regulating the membrane receptors, were identified in the P. lividus genome. In this way, the employment of the Mediterranean sea urchin for investigations and comparative analyses was empowered, leading to the explanation of cis-regulatory networks and their evolution in a key developmental model occupying an important evolutionary position with respect to vertebrates and humans.

Comparison of phagocytosis in three Caribbean Sea urchins

In 1983 large numbers of the sea urchin Diadema antillarum unexplainably began showing signs of illness and dying in the Caribbean, and over the next year they came close to extinction, making it one of the worst mass mortality events on record. Present evidence suggests a water-borne pathogen as the etiological agent. Decades later Diadema densities remain low, and its near extinction has been a major factor in transforming living coral reefs in the Caribbean to barren algae-covered rock. In the ensuing decades, no solid explanation has been found to the questions: what killed Diadema; why did Diadema succumb while other species of urchins on the same reefs did not; and why has Diadema still not recovered? A recent hypothesis posited by our lab as to Diadema's vulnerability was directed at possible compromised immunity in Diadema, and experimental results found a significantly impaired humoral response to a key component of gram-negative bacteria. Here we use flow cytometry to examine the cellular arm of invertebrate immunity. We performed cytotoxicity and phagocytosis assays as a measure of the cellular immune responses of cells from Diadema and two other species of sea urchins not affected by the die-off. Despite our previous findings of in impaired humoral response, our study found no apparent difference in the cellular phagocytic response of Diadema compared to the other urchin species studied.

Deep evolutionary origins of neurobiology: Turning the essence of 'neural' upside-down

It is generally assumed, both in common-sense argumentations and scientific concepts, that brains and neurons represent late evolutionary achievements which are present only in more advanced animals. Here we overview recently published data clearly revealing that our understanding of bacteria, unicellular eukaryotic organisms, plants, brains and neurons, rooted in the Aristotelian philosophy is flawed. Neural aspects of biological systems are obvious already in bacteria and unicellular biological units such as sexual gametes and diverse unicellular eukaryotic organisms. Altogether, processes and activities thought to represent evolutionary 'recent' specializations of the nervous system emerge rather to represent ancient and fundamental cell survival processes.

Proteolytic cascades and their involvement in invertebrate immunity

Bacteria and other potential pathogens are cleared rapidly from the body fluids of invertebrates by the immediate response of the innate immune system. Proteolytic cascades, following their initiation by pattern recognition proteins, control several such reactions, notably coagulation, melanisation, activation of the Toll receptor and complement-like reactions. However, there is considerable variation among invertebrates and these cascades, although widespread, are not present in all phyla. In recent years, significant progress has been made in identifying and characterizing these cascades in insects. Notably, recent work has identified several connections and shared principles among the different pathways, suggesting that cross-talk between them may be common.

Phosphoproteomes of Strongylocentrotus purpuratus shell and tooth matrix: identification of a major acidic sea urchin tooth phosphoprotein, phosphodontin

BACKGROUND

Sea urchin is a major model organism for developmental biology and biomineralization research. However, identification of proteins involved in larval skeleton formation and mineralization processes in the embryo and adult, and the molecular characterization of such proteins, has just gained momentum with the sequencing of the Strongylocentrotus purpuratus genome and the introduction of high-throughput proteomics into the field.

RESULTS

The present report contains the determination of test (shell) and tooth organic matrix phosphoproteomes. Altogether 34 phosphoproteins were identified in the biomineral organic matrices. Most phosphoproteins were specific for one compartment, only two were identified in both matrices. The sea urchin phosphoproteomes contained several obvious orthologs of mammalian proteins, such as a Src family tyrosine kinase, protein kinase C-delta 1, Dickkopf-1 and other signal transduction components, or nucleobindin. In most cases phosphorylation sites were conserved between sea urchin and mammalian proteins. However, the majority of phosphoproteins had no mammalian counterpart. The most interesting of the sea urchin-specific phosphoproteins, from the perspective of biomineralization research, was an abundant highly phosphorylated and very acidic tooth matrix protein composed of 35 very similar short sequence repeats, a predicted N-terminal secretion signal sequence, and an Asp-rich C-terminal motif, contained in [Glean3:18919].

CONCLUSIONS

The 64 phosphorylation sites determined represent the most comprehensive list of experimentally identified sea urchin protein phosphorylation sites at present and are an important addition to the recently analyzed Strongylocentrotus purpuratus shell and tooth proteomes. The identified phosphoproteins included a major, highly phosphorylated protein, [Glean3:18919], for which we suggest the name phosphodontin. Although not sequence-related to such highly phosphorylated acidic mammalian dental phosphoproteins as phosphoryn or dentin matrix protein-1, phosphodontin may perform similar functions in the sea urchin tooth. More than half of the detected proteins were not previously identified at the protein level, thus confirming the existence of proteins only known as genomic sequences previously.

Endocannabinoids: friends and foes of reproduction

Endocannabinoids are fatty acid amides like anandamide (AEA), and monoacylglycerols like 2-arachidonoylglycerol, that bind to cannabinoid, vanilloid and peroxisome proliferator-activated receptors. Their biological actions are controlled through not yet fully characterized cellular mechanisms. These compounds, together with their related enzymes, that include key proteins for the synthesis and degradation of endocannabinoids, cannabinoid and non-cannabinoid receptors, and purported membrane transporter(s), form the "endocannabinoid system (ECS)". In the past few years AEA and related ECS elements have emerged as essential players in various aspects of human reproduction, both for males and females. Here, the key features of the ECS and the potential of its components to direct human fertility towards a positive or negative end will be reviewed. In particular, the involvement of AEA and related ECS elements in regulating embryo oviductal transport, blastocyst implantation and placental development (in females), and sperm survival, motility, capacitation and acrosome reaction (in males) will be addressed, as well as the role of endocannabinoids in sperm-oviduct interactions. Additionally, the possibility that blood AEA and its hydrolase FAAH may represent reliable diagnostic markers of natural and assisted reproduction in humans will be discussed, along with the therapeutic exploitation of ECS-oriented drugs as useful fertility enhancers.