ESTs library from embryonic stages reveals tubulin and reflectin diversity in Sepia officinalis (Mollusca — Cephalopoda)

Exploration of chemosensory ionotropic receptors in cephalopods: the IR25 gene is expressed in the olfactory organs, suckers, and fins of Sepia officinalis

While they are mostly renowned for their visual capacities, cephalopods are also good at olfaction for prey, predator, and conspecific detection. The olfactory organs and olfactory cells are well described but olfactory receptors-genes and proteins-are still undescribed in cephalopods. We conducted a broad phylogenetic analysis of the ionotropic glutamate receptor family in mollusks (iGluR), especially to identify IR members (Ionotropic Receptors), a variant subfamily whose involvement in chemosensory functions has been shown in most studied protostomes. A total of 312 iGluRs sequences (including 111 IRs) from gastropods, bivalves, and cephalopods were identified and annotated. One orthologue of the gene coding for the chemosensory IR25 co-receptor has been found in Sepia officinalis (Soff-IR25). We searched for Soff-IR25 expression at the cellular level by in situ hybridization in whole embryos at late stages before hatching. Expression was observed in the olfactory organs, which strongly validates the chemosensory function of this receptor in cephalopods. Soff-IR25 was also detected in the developing suckers, which suggests that the unique « taste by touch » behavior that cephalopods execute with their arms and suckers share features with olfaction. Finally, Soff-IR25 positive cells were unexpectedly found in fins, the two posterior appendages of cephalopods, mostly involved in locomotory functions. This result opens new avenues of investigation to confirm fins as additional chemosensory organs in cephalopods.

Cephalopod Biology: At the Intersection Between Genomic and Organismal Novelties

Cephalopods are resourceful marine predators that have fascinated generations of researchers as well as the public owing to their advanced behavior, complex nervous system, and significance in evolutionary studies. Recent advances in genomics have accelerated the pace of cephalopod research. Many traditional areas focusing on evolution, development, behavior, and neurobiology, primarily on the morphological level, are now transitioning to molecular approaches. This review addresses the recent progress and impact of genomic and other molecular resources on research in cephalopods. We outline several key directions in which significant progress in cephalopod research is expected and discuss its impact on our understanding of the genetic background behind cephalopod biology and beyond.

Reversion to developmental pathways underlies rapid arm regeneration in juvenile European cuttlefish, Sepia officinalis (Linnaeus 1758)

Coleoid cephalopods, including the European cuttlefish (Sepia officinalis), possess the remarkable ability to fully regenerate an amputated arm with no apparent fibrosis or loss of function. In model organisms, regeneration usually occurs as the induction of proliferation in differentiated cells. In rare circumstances, regeneration can be the product of naïve progenitor cells proliferating and differentiating de novo . In any instance, the immune system is an important factor in the induction of the regenerative response. Although the wound response is well-characterized, little is known about the physiological pathways utilized by cuttlefish to reconstruct a lost arm. In this study, the regenerating arms of juvenile cuttlefish, with or without exposure at the time of injury to sterile bacterial lipopolysaccharide extract to provoke an antipathogenic immune response, were assessed for the transcription of early tissue lineage developmental genes, as well as histological and protein turnover analyses of the resulting regenerative process. The transient upregulation of tissue-specific developmental genes and histological characterization indicated that coleoid arm regeneration is a stepwise process with staged specification of tissues formed de novo, with immune activation potentially affecting the timing but not the result of this process. Together, the data suggest that rather than inducing proliferation of mature cells, developmental pathways are reinstated, and that a pool of naïve progenitors at the blastema site forms the basis for this regeneration.

Bioactive Silk-Based Nerve Guidance Conduits for Augmenting Peripheral Nerve Repair

Repair of peripheral nerve injuries depends upon complex biology stemming from the manifold and challenging injury-healing processes of the peripheral nervous system. While surgical treatment options are available, they tend to be characterized by poor clinical outcomes for the injured patients. This is particularly apparent in the clinical management of a nerve gap whereby nerve autograft remains the best clinical option despite numerous limitations; in addition, effective repair becomes progressively more difficult with larger gaps. Nerve conduit strategies based on tissue engineering approaches and the use of silk as scaffolding material have attracted much attention in recent years to overcome these limitations and meet the clinical demand of large gap nerve repair. This review examines the scientific advances made with silk-based conduits for peripheral nerve repair. The focus is on enhancing bioactivity of the conduits in terms of physical guidance cues, inner wall and lumen modification, and imbuing novel conductive functionalities.

Eye Development in Sepia officinalis Embryo: What the Uncommon Gene Expression Profiles Tell Us about Eye Evolution

In metazoans, there is a remarkable diversity of photosensitive structures; their shapes, physiology, optical properties, and development are different. To approach the evolution of photosensitive structures and visual function, cephalopods are particularly interesting organisms due to their most highly centralized nervous system and their camerular eyes which constitute a convergence with those of vertebrates. The eye morphogenesis in numerous metazoans is controlled mainly by a conserved Retinal Determination Gene Network (RDGN) including pax, six, eya, and dac playing also key developmental roles in non-retinal structures and tissues of vertebrates and Drosophila. Here we have identified and explored the role of Sof-dac, Sof-six1/2, Sof-eya in eye morphogenesis, and nervous structures controlling the visual function in Sepia officinalis. We compare that with the already shown expressions in eye development of Sof-otx and Sof-pax genes. Rhodopsin is the pigment responsible for light sensitivity in metazoan, which correlate to correlate visual function and eye development. We studied Sof-rhodopsin expression during retina differentiation. By in situ hybridization, we show that (1) all of the RDGN genes, including Sof-pax6, are expressed in the eye area during the early developmental stages but they are not expressed in the retina, unlike Sof-otx, which could have a role in retina differentiation; (2) Sof-rhodopsin is expressed in the retina just before vision gets functional, from stage 23 to hatching. Our results evidence a role of Sof-six1/2, Sof-eya, and Sof-dac in eye development. However, the gene network involved in the retinal photoreceptor differentiation remains to be determined. Moreover, for the first time, Sof-rhodopsin expression is shown in the embryonic retina of cuttlefish suggesting the evolutionary conservation of the role of rhodopsin in visual phototransduction within metazoans. These findings are correlated with the physiological and behavioral observations suggesting that S. officinalis is able to react to light stimuli from stage 25 of organogenesis on, as soon as the first retinal pigments appear.

The Pax gene family: Highlights from cephalopods

Pax genes play important roles in Metazoan development. Their evolution has been extensively studied but Lophotrochozoa are usually omitted. We addressed the question of Pax paralog diversity in Lophotrochozoa by a thorough review of available databases. The existence of six Pax families (Pax1/9, Pax2/5/8, Pax3/7, Pax4/6, Paxβ, PoxNeuro) was confirmed and the lophotrochozoan Paxβ subfamily was further characterized. Contrary to the pattern reported in chordates, the Pax2/5/8 family is devoid of homeodomain in Lophotrochozoa. Expression patterns of the three main pax classes (pax2/5/8, pax3/7, pax4/6) during Sepia officinalis development showed that Pax roles taken as ancestral and common in metazoans are modified in S. officinalis, most likely due to either the morphological specificities of cephalopods or to their direct development. Some expected expression patterns were missing (e.g. pax6 in the developing retina), and some expressions in unexpected tissues have been found (e.g. pax2/5/8 in dermal tissue and in gills). This study underlines the diversity and functional plasticity of Pax genes and illustrates the difficulty of using probable gene homology as strict indicator of homology between biological structures.

Analysis of Gene Expression in an Inbred Line of Soft-Shell Clams (Mya arenaria) Displaying Growth Heterosis: Regulation of Structural Genes and the NOD2 Pathway

Mya arenaria is a bivalve mollusk of commercial and economic importance, currently impacted by ocean warming, acidification, and invasive species. In order to inform studies on the growth of M. arenaria, we selected and inbred a population of soft-shell clams for a fast-growth phenotype. This population displayed significantly faster growth (p < 0.0001), as measured by 35.4% greater shell size. To assess the biological basis of this growth heterosis, we characterized the complete transcriptomes of six individuals and identified differentially expressed genes by RNAseq. Pathways differentially expressed included structural gene pathways. Also differentially expressed was the nucleotide-binding oligomerization domain 2 (NOD2) receptor pathway that contributes to determination of growth, immunity, apoptosis, and proliferation. NOD2 pathway members that were upregulated included a subset of isoforms of RIPK2 (mean 3.3-fold increase in expression), ERK/MAPK14 (3.8-fold), JNK/MAPK8 (4.1-fold), and NFκB (4.08-fold). These transcriptomes will be useful resources for both the aquaculture community and researchers with an interest in mollusks and growth heterosis.

Eye development and photoreceptor differentiation in the cephalopod Doryteuthis pealeii

Photoreception is a ubiquitous sensory ability found across the Metazoa, and photoreceptive organs are intricate and diverse in their structure. Although the morphology of the compound eye in Drosophila and the single-chambered eye in vertebrates have elaborated independently, the amount of conservation within the 'eye' gene regulatory network remains controversial, with few taxa studied. To better understand the evolution of photoreceptive organs, we established the cephalopod Doryteuthis pealeii as a lophotrochozoan model for eye development. Utilizing histological, transcriptomic and molecular assays, we characterize eye formation in Doryteuthis pealeii Through lineage tracing and gene expression analyses, we demonstrate that cells expressing Pax and Six genes incorporate into the lens, cornea and iris, and the eye placode is the sole source of retinal tissue. Functional assays demonstrate that Notch signaling is required for photoreceptor cell differentiation and retinal organization. This comparative approach places the canon of eye research in traditional models into perspective, highlighting complexity as a result of both conserved and convergent mechanisms.

Nervous system development in cephalopods: How egg yolk-richness modifies the topology of the mediolateral patterning system

Cephalopods possess the most complex centralized nervous system among molluscs and the molecular determinants of its development have only begun to be explored. To better understand how evolved their brain and body axes, we studied Sepia officinalis embryos and investigated the expression patterns of neural regionalization genes involved in the mediolateral patterning of the neuroectoderm in model species. SoxB1 expression reveals that the embryonic neuroectoderm is made of several distinct territories that constitute a large part of the animal pole disc. Concentric nkx2.1, pax6/gsx, and pax3/7/msx/pax2/5/8 positive domains subdivide this neuroectoderm. Looking from dorsal to ventral sides, the sequence of these expressions is reminiscent of the mediolateral subdivision in model species, which provides good evidence for "mediolateral patterning" conservation in cephalopods. A specific feature of cephalopod development, however, includes an unconventional orientation to this mediolateral sequence: median markers (like nkx2.1) are unexpectedly expressed at the periphery of the cuttlefish embryo and lateral markers (like Pax3/7) are expressed centrally. As the egg is rich with yolk, the lips of the blastopore (that classically organizes the neural midline) remain unclosed at the lateral side of the animal pole until late stages of organogenesis, therefore reversing the whole embryo topology. These findings confirm - by means of molecular tools - the location of both ventral and dorsal poles in cephalopod embryos.

Reflectin as a Material for Neural Stem Cell Growth

Cephalopods possess remarkable camouflage capabilities, which are enabled by their complex skin structure and sophisticated nervous system. Such unique characteristics have in turn inspired the design of novel functional materials and devices. Within this context, recent studies have focused on investigating the self-assembly, optical, and electrical properties of reflectin, a protein that plays a key role in cephalopod structural coloration. Herein, we report the discovery that reflectin constitutes an effective material for the growth of human neural stem/progenitor cells. Our findings may hold relevance both for understanding cephalopod embryogenesis and for developing improved protein-based bioelectronic devices.

POU genes are expressed during the formation of individual ganglia of the cephalopod central nervous system

Background

Among the Lophotrochozoa, cephalopods possess the highest degree of central nervous system (CNS) centralization and complexity. Although the anatomy of the developing cephalopod CNS has been investigated, the developmental mechanisms underlying brain development and evolution are unknown. POU genes encode key transcription factors controlling nervous system development in a range of bilaterian species, including lophotrochozoans. In this study, we investigate the expression of POU genes during early development of the pygmy squid Idiosepius notoides and make comparisons with other bilaterians to reveal whether these genes have conserved or divergent roles during CNS development in this species.

Results

POU2, POU3, POU4 and POU6 orthologs were identified in transcriptomes derived from developmental stages and adult brain tissue of I. notoides. All four POU gene orthologs are expressed in different spatiotemporal combinations in the early embryo. Ino-POU2 is expressed in the gills and the palliovisceral, pedal, and optic ganglia of stage 19 to 20 embryos, whereas the cerebral and palliovisceral ganglia express Ino-POU3. Ino-POU4 is expressed in the optic and palliovisceral ganglia and the arms/intrabrachial ganglia of stage 19 to 20 individuals. Ino-POU6 is expressed in the palliovisceral ganglia during early development. In stage 25 embryos expression domains include the intrabrachial ganglia (Ino-POU3) and the pedal ganglia (Ino-POU6). All four POU genes are strongly expressed in large areas of the brain of stage 24 to 26 individuals. Expression could not be detected in late prehatching embryos (approximately stage 27 to 30).

Conclusions

The expression of four POU genes in unique spatiotemporal combinations during early neurogenesis and sensory organ development of I. notoides suggests that they fulfill distinct tasks during early brain development. Comparisons with other bilaterian species reveal that POU gene expression is associated with anteriormost neural structures, even between animals for which these structures are unlikely to be homologous. Within lophotrochozoans, POU3 and POU4 are the only two genes that have been comparatively investigated. Their expression patterns are broadly similar, indicating that the increased complexity of the cephalopod brain is likely due to other unknown factors.

Emergence of sensory structures in the developing epidermis in sepia officinalis and other coleoid cephalopods

Embryonic cuttlefish can first respond to a variety of sensory stimuli during early development in the egg capsule. To examine the neural basis of this ability, we investigated the emergence of sensory structures within the developing epidermis. We show that the skin facing the outer environment (not the skin lining the mantle cavity, for example) is derived from embryonic domains expressing the Sepia officinalis ortholog of pax3/7, a gene involved in epidermis specification in vertebrates. On the head, they are confined to discrete brachial regions referred to as "arm pillars" that expand and cover Sof-pax3/7-negative head ectodermal tissues. As revealed by the expression of the S. officinalis ortholog of elav1, an early marker of neural differentiation, the olfactory organs first differentiate at about stage 16 within Sof-pax3/7-negative ectodermal regions before they are covered by the definitive Sof-pax3/7-positive outer epithelium. In contrast, the eight mechanosensory lateral lines running over the head surface and the numerous other putative sensory cells in the epidermis, differentiate in the Sof-pax3/7-positive tissues at stages ∼24-25, after they have extended over the entire outer surfaces of the head and arms. Locations and morphologies of the various sensory cells in the olfactory organs and skin were examined using antibodies against acetylated tubulin during the development of S. officinalis and were compared with those in hatchlings of two other cephalopod species. The early differentiation of olfactory structures and the peculiar development of the epidermis with its sensory cells provide new perspectives for comparisons of developmental processes among molluscs.

Diversity of the RFamide Peptide Family in Mollusks

Since the initial characterization of the cardioexcitatory peptide FMRFamide in the bivalve mollusk Macrocallista nimbosa, a great number of FMRFamide-like peptides (FLPs) have been identified in mollusks. FLPs were initially isolated and molecularly characterized in model mollusks using biochemical methods. The development of recombinant technologies and, more recently, of genomics has boosted knowledge on their diversity in various mollusk classes. Today, mollusk FLPs represent approximately 75 distinct RFamide peptides that appear to result from the expression of only five genes: the FMRFamide-related peptide gene, the LFRFamide gene, the luqin gene, the neuropeptide F gene, and the cholecystokinin/sulfakinin gene. FLPs display a complex spatiotemporal pattern of expression in the central and peripheral nervous system. Working as neurotransmitters, neuromodulators, or neurohormones, FLPs are involved in the control of a great variety of biological and physiological processes including cardiovascular regulation, osmoregulation, reproduction, digestion, and feeding behavior. From an evolutionary viewpoint, the major challenge will then logically concern the elucidation of the FLP repertoire of orphan mollusk classes and the way they are functionally related. In this respect, deciphering FLP signaling pathways by characterizing the specific receptors these peptides bind remains another exciting objective.

Delayed and asynchronous ganglionic maturation during cephalopod neurogenesis as evidenced by Sof-elav1 expression in embryos of Sepia officinalis (Mollusca, Cephalopoda)

Among the Lophotrochozoa, centralization of the nervous system reaches an exceptional level of complexity in cephalopods, where the typical molluscan ganglia become highly developed and fuse into hierarchized lobes. It is known that ganglionic primordia initially emerge early and simultaneously during cephalopod embryogenesis but no data exist on the process of neuron differentiation in this group. We searched for members of the elav/hu family in the cuttlefish Sepia officinalis, since they are one of the first genetic markers of postmitotic neural cells. Two paralogs were identified and the expression of the most neural-specific gene, Sof-elav1, was characterized during embryogenesis. Sof-elav1 is expressed in all ganglia at one time of development, which provides the first genetic map of neurogenesis in a cephalopod. Our results unexpectedly revealed that Sof-elav1 expression is not similar and not coordinated in all the prospective ganglia. Both palliovisceral ganglia show extensive Sof-elav1 expression soon after emergence, showing that most of their cells differentiate into neurons at an early stage. On the contrary, other ganglia, and especially both cerebral ganglia that contribute to the main parts of the brain learning centers, show a late extensive Sof-elav1 expression. These delayed expressions in ganglia suggest that most ganglionic cells retain their proliferative capacities and postpone differentiation. In other molluscs, where a larval nervous system predates the development of the definitive adult nervous system, cerebral ganglia are among the first to mature. Thus, such a difference may constitute a cue in understanding the peculiar brain evolution in cephalopods.

Reflectin genes and development of iridophore patterns in Sepia officinalis embryos (Mollusca, Cephalopoda)

BACKGROUND

In the cuttlefish Sepia officinalis, iridescence is known to play a role in patterning and communication. In iridophores, iridosomes are composed of reflectins, a protein family, which show great diversity in all cephalopod species. Iridosomes are established before hatching, but very little is known about how these cells are established, their distribution in embryos, or the contribution of each reflectin gene to iridosome structures.

RESULTS

Six reflectin genes are expressed during the development of iridosomes in Sepia officinalis. We show that they are expressed in numerous parts of the body before hatching. Evidence of the colocalization of two different genes of reflectin was found. Curiously, reflectin mRNA expression was no longer detectable at the time of hatchling, while reflectin proteins were present and gave rise to visible iridescence.

CONCLUSION

These data suggest that several different forms of reflectins are simultaneously used to produce iridescence in S. officinalis and that mRNA production and translation are decoupled in time during iridosome development.

Cephalopod genomics: A plan of strategies and organization

The Cephalopod Sequencing Consortium (CephSeq Consortium) was established at a NESCent Catalysis Group Meeting, “Paths to Cephalopod Genomics- Strategies, Choices, Organization,” held in Durham, North Carolina, USA on May 24-27, 2012. Twenty-eight participants representing nine countries (Austria, Australia, China, Denmark, France, Italy, Japan, Spain and the USA) met to address the pressing need for genome sequencing of cephalopod mollusks. This group, drawn from cephalopod biologists, neuroscientists, developmental and evolutionary biologists, materials scientists, bioinformaticians and researchers active in sequencing, assembling and annotating genomes, agreed on a set of cephalopod species of particular importance for initial sequencing and developed strategies and an organization (CephSeq Consortium) to promote this sequencing. The conclusions and recommendations of this meeting are described in this white paper.

Mechanisms of protein degradation in mantle muscle and proposed gill remodeling in starved Sepia officinalis

Cephalopods have relatively high rates of protein synthesis compared to rates of protein degradation, along with minimal carbohydrate and lipid reserves. During food deprivation on board protein is catabolized as a metabolic fuel. The aim of the current study was to assess whether biochemical indices of protein synthesis and proteolytic mechanisms were altered in cuttlefish, Sepia officinalis, starved for 7 days. In mantle muscle, food deprivation is associated with a decrease in protein synthesis, as indicated by a decrease in the total RNA level and dephosphorylation of key signaling molecules, such as the eukaryote binding protein, 4E-BP1 (regulator of translation) and Akt. The ubiquitination-proteasome system (UPS) is activated as shown by an increase in the levels of proteasome β-subunit mRNA, polyubiquitinated protein, and polyubiquitin mRNA. As well, cathepsin activity levels are increased, suggesting increased proteolysis through the lysosomal pathway. Together, these mechanisms could supply amino acids as metabolic fuels. In gill, the situation is quite different. It appears that during the first stages of starvation, both protein synthesis and protein degradation are enhanced in gill. This is based upon increased phosphorylation of 4E-BP1 and enhanced levels of UPS indicators, especially 20S proteasome activity and polyubiquitin mRNA. It is proposed that an increased protein turnover is related to gill remodeling perhaps to retain essential hemolymph-borne compounds.

orthodenticle/otx ortholog expression in the anterior brain and eyes of Sepia officinalis (Mollusca, Cephalopoda)

The origin of cerebral structures is a major issue in both developmental and evolutionary biology. Among Lophotrochozoans, cephalopods present both a derived nervous system and an original body plan, therefore they constitute a key model to study the evolution of nervous system and molecular processes that control the neural organization. We characterized a partial sequence of an ortholog of otx2 in Sepia officinalis embryos, a gene specific to the anterior nervous system and eye development. By in situ hybridization, we assessed the expression pattern of otx2 during S. officinalis organogenesis and we showed that otx is expressed (1) in the eyes, from early to late developmental stages as observed in other species (2) in the nervous system during late developmental stages. The otx ortholog does not appear to be required for the precocious emergence of the nervous ganglia in cephalopods and is later expressed only in the most anterior ganglia of the future brain. Finally, otx expression becomes restricted to localized part of the brain, where it could be involved in the functional specification of the central nervous system of S. officinalis. These results suggest a conserved involvement of otx in eye maturation and development of the anterior neural structures in S. officinalis.