Unusual Evolution of Cephalopod Tryptophan Indole-Lyases.

Tryptophan indole-lyase (TIL), a pyridoxal-5-phosphate-dependent enzyme, catalyzes the hydrolysis of L-tryptophan (L-Trp) to indole and ammonium pyruvate. TIL is widely distributed among bacteria and bacterial TILs consist of a D2-symmetric homotetramer. On the other hand, TIL genes are also present in several metazoans. Cephalopods have two TILs, TILα and TILß, which are believed to be derived from a gene duplication that occurred before octopus and squid diverged. However, both TILα and TILß individually contain disruptive amino acid substitutions for TIL activity, and neither was active when expressed alone. When TILα and TILß were coexpressed, however, they formed a heterotetramer that exhibited low TIL activity. The loss of TIL activity of the heterotetramer following site-directed mutagenesis strongly suggests that the active heterotetramer contains the TILα/TILß heterodimer. Metazoan TILs generally have lower kcat values for L-Trp than those of bacterial TILs, but such low TIL activity may be rather suitable for metazoan physiology, where L-Trp is in high demand. Therefore, reduced activity may have been a less likely target for purifying selection in the evolution of cephalopod TILs. Meanwhile, the unusual evolution of cephalopod TILs may indicate the difficulty of post-gene duplication evolution of enzymes with catalytic sites contributed by multiple subunits, such as TIL.

RNA recoding in cephalopods tailors microtubule motor protein function.

RNA editing is a widespread epigenetic process that can alter the amino acid sequence of proteins, termed "recoding." In cephalopods, most transcripts are recoded, and recoding is hypothesized to be an adaptive strategy to generate phenotypic plasticity. However, how animals use RNA recoding dynamically is largely unexplored. We investigated the function of cephalopod RNA recoding in the microtubule motor proteins kinesin and dynein. We found that squid rapidly employ RNA recoding in response to changes in ocean temperature, and kinesin variants generated in cold seawater displayed enhanced motile properties in single-molecule experiments conducted in the cold. We also identified tissue-specific recoded squid kinesin variants that displayed distinct motile properties. Finally, we showed that cephalopod recoding sites can guide the discovery of functional substitutions in non-cephalopod kinesin and dynein. Thus, RNA recoding is a dynamic mechanism that generates phenotypic plasticity in cephalopods and can inform the characterization of conserved non-cephalopod proteins.

In Vivo Mercury (De)Methylation Metabolism in Cephalopods under Different pCO2 Scenarios.

This work quantified the accumulation efficiencies of Hg in cuttlefish, depending on both organic (MeHg) and inorganic (Hg(II)) forms, under increased pCO2 (1600 µatm). Cuttlefish were fed with live shrimps injected with two Hg stable isotopic tracers (Me202Hg and 199Hg(II)), which allowed for the simultaneous quantification of internal Hg accumulation, Hg(II) methylation, and MeHg demethylation rates in different organs. Results showed that pCO2 had no impact on Hg bioaccumulation and organotropism, and both Hg and pCO2 did not influence the microbiota diversity of gut and digestive gland. However, the results also demonstrated that the digestive gland is a key organ for in vivo MeHg demethylation. Consequently, cuttlefish exposed to environmental levels of MeHg could exhibit in vivo MeHg demethylation. We hypothesize that in vivo MeHg demethylation could be due to biologically induced reactions or to abiotic reactions. This has important implications as to how some marine organisms may respond to future ocean change and global mercury contamination.

Proteomics of Shell Matrix Proteins from the Cuttlefish Bone Reveals Unique Evolution for Cephalopod Biomineralization.

In contrast to the external shells in bivalves and gastropods, most cephalopods are missing this external protection. The cuttlefish, belonging to class cephalopod, has an internal biomineralized structure made of mainly calcium carbonate for controlling buoyancy. However, the macromolecules, especially proteins that control cuttlebone mineral formation, are not sufficiently understood, limiting our understanding of the evolution of this internal shell. In this study, we extracted proteins from the cuttlebone of pharaoh cuttlefish Sepia pharaonis and performed liquid chromatography-tandem mass spectrometry to identify the shell matrix proteins (SMPs). In total, 41 SMPs were identified. Among them, hemocyanin, an oxygen-carrying protein, was the most abundant SMP. By comparison with SMPs of other marine biominerals, hemocyanin, apolipophorin, soul domain proteins, transferrin, FL-rich, and enolase were found to be unique to the cuttlebone. In contrast, typical SMPs of external shells such as carbonic anhydrase complement control protein, fibronectin type III, and G/A-rich proteins were lacking from the cuttlebone. Furthermore, the cluster analysis of biomineral SMPs suggests that the SMP repertoire of the cuttlebone does not resemble that of other species with external shells. Taken together, this study implies a potential relationship of the cuttlefish internal shell with other internal biominerals, which highlights a unique shell evolutionary pathway in invertebrates.

Epigenetic machinery is functionally conserved in cephalopods.

BACKGROUND: Epigenetic regulatory mechanisms are divergent across the animal kingdom, yet these mechanisms are not well studied in non-model organisms. Unique features of cephalopods make them attractive for investigating behavioral, sensory, developmental, and regenerative processes, and recent studies have elucidated novel features of genome organization and gene and transposon regulation in these animals. However, it is not known how epigenetics regulates these interesting cephalopod features. We combined bioinformatic and molecular analysis of Octopus bimaculoides to investigate the presence and pattern of DNA methylation and examined the presence of DNA methylation and 3 histone post-translational modifications across tissues of three cephalopod species. RESULTS: We report a dynamic expression profile of the genes encoding conserved epigenetic regulators, including DNA methylation maintenance factors in octopus tissues. Levels of 5-methyl-cytosine in multiple tissues of octopus, squid, and bobtail squid were lower compared to vertebrates. Whole genome bisulfite sequencing of two regions of the brain and reduced representation bisulfite sequencing from a hatchling of O. bimaculoides revealed that less than 10% of CpGs are methylated in all samples, with a distinct pattern of 5-methyl-cytosine genome distribution characterized by enrichment in the bodies of a subset of 14,000 genes and absence from transposons. Hypermethylated genes have distinct functions and, strikingly, many showed similar expression levels across tissues while hypomethylated genes were silenced or expressed at low levels. Histone marks H3K27me3, H3K9me3, and H3K4me3 were detected at different levels across tissues of all species. CONCLUSIONS: Our results show that the DNA methylation and histone modification epigenetic machinery is conserved in cephalopods, and that, in octopus, 5-methyl-cytosine does not decorate transposable elements, but is enriched on the gene bodies of highly expressed genes and could cooperate with the histone code to regulate tissue-specific gene expression.

A hierarchy in clusters of cephalopod mRNA editing sites.

RNA editing in the form of substituting adenine with inosine (A-to-I editing) is the most frequent type of RNA editing in many metazoan species. In most species, A-to-I editing sites tend to form clusters and editing at clustered sites depends on editing of the adjacent sites. Although functionally important in some specific cases, A-to-I editing usually is rare. The exception occurs in soft-bodied coleoid cephalopods, where tens of thousands of potentially important A-to-I editing sites have been identified, making coleoids an ideal model for studying of properties and evolution of A-to-I editing sites. Here, we apply several diverse techniques to demonstrate a strong tendency of coleoid RNA editing sites to cluster along the transcript. We show that clustering of editing sites and correlated editing substantially contribute to the transcriptome diversity that arises due to extensive RNA editing. Moreover, we identify three distinct types of editing site clusters, varying in size, and describe RNA structural features and mechanisms likely underlying formation of these clusters. In particular, these observations may explain sequence conservation at large distances around editing sites and the observed dependency of editing on mutations in the vicinity of editing sites.

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 ¼ 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.

A survey of arsenic, mercury, cadmium, and lead residues in seafood (fish, crustaceans, and cephalopods) from the south-eastern Mediterranean Sea.

Seafood is capable of bioaccumulating heavy metals (HM), making it a potentially major dietary source of HM for humans. Presently, little data exists on seafood from the eastern-most boundary of the Mediterranean Sea. This study aims to provide exposure insight of the Israeli population to HM through the consumption of locally caught seafood by assessing the levels of arsenic, mercury, cadmium, and lead in raw tissues of seafood. A wide survey of local fisheries was conducted providing 296 samples from 11 different species, including seven fish, two crustacean, and two cephalopod species. Total arsenic, cadmium, and lead were analyzed by graphite-furnace atomic absorption. Total mercury was measured by cold-vapor mercury analyzer. Arsenic speciation was performed by anion chromatography-inductively coupled plasma sector field mass spectrometry. Results suggested that the total arsenic concentrations were significantly higher in crustaceans and cephalopods than fish. Arsenic speciation revealed two samples that exceed 1 mg/kg of inorganic arsenic, whereas methylated arsenic was below the detection limit. Elevated mercury levels were detected in the commercial benthic species Mullus barbatus (red mullet), cadmium was detected in one-third of the samples, and lead detected in eight samples. Comparing the results to health guidelines, 99.4% of seafood tested in this study abide with acceptable levels of heavy metals in seafood, as defined by both Israeli and European Union guidelines.

Biomimetic Colorants and Coatings Designed with Cephalopod-Inspired Nanocomposites.

Brilliant and dynamic colors in nature have stimulated the design of dyes and pigments with broad applications ranging from electronic displays to apparel. Inspired by the nanostructured pigment granules present in cephalopod chromatophore organs, we describe the design and fabrication of biohybrid colorants containing the cephalopod-specific pigment, xanthommatin (Xa), encased within silica-based nanostructures. We employed a biomimetic approach to encapsulate Xa with amine-terminated polyamidoamine (PAMAM) dendrimer templates, which helped stabilize the pigment during encapsulation. Depending on the concentration of Xa used in the reaction, the resultant biohybrid nanomaterials generated a range of neutral colors of differing hues. When applied as coatings, these colorants can be triggered to change color from yellow/gold to red in the presence of a chemical reducing agent, as we leverage the natural redox-dependent color change of Xa. Altogether, these capabilities demonstrated the ability to process biochromes like Xa as nanomaterials that can be applied as coatings with a tunable and dynamic range.

Diet and life history reduce interspecific and intraspecific competition among three sympatric Arctic cephalopods.

Trophic niche and diet comparisons among closely sympatric marine species are important to understand complex food webs, particularly in regions most affected by climate change. Using stable isotope analyses, all ontogenetic stages of three sympatric species of Arctic cephalopods (genus Rossia) were studied to assess inter- and intraspecific competition with niche and diet overlap and partitioning in West Greenland and the Barents Sea. Seven traits related to resource and habitat utilization were identified in Rossia: no trait was shared by all three species. High boreal R. megaptera and Arctic endemic R. moelleri shared three traits with each other, while both R. megaptera and R. moelleri shared only two unique traits each with widespread boreal-Arctic R. palpebrosa. Thus all traits formed fully uncrossing pattern with each species having unique strategy of resource and habitat utilization. Predicted climate changes in the Arctic would have an impact on competition among Rossia with one potential 'winner' (R. megaptera in the Barents Sea) but no potential 'losers'.

Concentrations of trace elements in the organs of commercially exploited crustaceans and cephalopods caught in the waters of Thoothukudi, South India.

Concentrations of trace elements (arsenic, cadmium, mercury, and lead) in tissues (muscle, gills, and digestive gland) of three commercially exploited crustaceans (Portunus sanguinolentus, Charybdis natator, and Penaeus semisulcatus) and three cephalopods (Doryteuthis sibogae, Sepia pharaonis, and Cistopus indicus) were examined. The animals were captured in the waters of Thoothukudi, and the tissues of six individuals of each species were analyzed using ICP-MS. The highest concentrations of arsenic (16.5 µg/g) and mercury (0.052 µg/g) were recorded in the digestive gland of C. natator, and cadmium (69.9 µg/g) and lead (0.351 µg/g) in the digestive gland of S. pharaonis. The edible portion of the crustaceans and cephalopods contained lower concentrations of trace elements, and these were below allowable limits set by the European Union. The edible parts of the investigated samples are safe for human consumption, but accidental contamination of the edible tissues with material from the digestive glands could lead to concerns relating to metal toxicity.

Chamber volume development, metabolic rates, and selective extinction in cephalopods.

Reconstructing the physiology of extinct organisms is key to understanding mechanisms of selective extinction during biotic crises. Soft tissues of extinct organisms are rarely preserved and, therefore, a proxy for physiological aspects is needed. Here, we examine whether cephalopod conchs yield information about their physiology by assessing how the formation of chambers respond to external stimuli such as environmental changes. We measured chamber volume through ontogeny to detect differences in the pattern of chamber volume development in nautilids, coleoids, and ammonoids. Results reveal that the differences between ontogenetic trajectories of these cephalopods involve the presence or absence of abrupt decreases of chamber volume. Accepting the link between metabolic rate and growth, we assume that this difference is rooted in metabolic rates that differ between cephalopod clades. High metabolic rates combined with small hatching size in ammonoids as opposed to lower metabolic rates and much larger hatchlings in most nautilids may explain the selective extinction of ammonoids as a consequence of low food availability at the end of the Cretaceous.

Identification, characterization and mRNA transcript abundance profiles of estrogen related receptor (ERR) in Sepiella japonica imply its possible involvement in female reproduction.

Estrogen related receptors (ERRs) are widely detected in vertebrates and apparently have functions in reproduction. The functions of ERRs in reproduction of invertebrates, especially in mollusk cephalopods, are largely unknown. In the present study, An homologue of vertebrate ERR gene was first cloned from female Sepiella japonica, an important Cephalopod species in coastal water of China. Results indicate the S. japonica ERR (sjERR) gene is comprised of 1513 nucleotides, containing a 1389 bp open reading frame, which encode for 463 amino acid (aa) residues. The deduced sjERR protein possessed six typical nuclear receptors (NR) domains (A-F), with a DNA-binding domain (DBD) and a highly conserved ligand-binding domain (LBD), compared to the other molluscan ERRs. Results from tissue analyses indicated that sjERR mRNA transcript abundance was in largest amounts in tissues of the brain, liver, ovary that are possibly involved in reproduction. The sjERR mRNA transcript abundance was temporally regulated during the different sexual maturation phases of female S. japonica and was affected by in vivo administrations of vertebrate steroid estradiol-17ß (E2). An in vivo knockdown of sjERR gene expression resulted in a marked down-regulation in expression of genes involved in ovarian development, such as Vitellogenin, CDK1, and Cyclin B, indicating there is a possible involvement of sjERR in reproduction. Both fusion protein transient transfections and immunohistochemical analyses indicated a presence of sjERR in the nucleus, implying a possible mechanism of action of the sjERR in the nucleus through activation of specific gene transcriptions.

Calibration between trigger and color: Neutralization of a genetically encoded coulombic switch and dynamic arrest precisely tune reflectin assembly.

Reflectin proteins are widely distributed in reflective structures in cephalopods. However, only in loliginid squids are they and the subwavelength photonic structures they control dynamically tunable, driving changes in skin color for camouflage and communication. The reflectins are block copolymers with repeated canonical domains interspersed with cationic linkers. Neurotransmitter-activated signal transduction culminates in catalytic phosphorylation of the tunable reflectins' cationic linkers; the resulting charge neutralization overcomes coulombic repulsion to progressively allow condensation, folding, and assembly into multimeric spheres of tunable well-defined size and low polydispersity. Here, we used dynamic light scattering, transmission EM, CD, atomic force microscopy, and fluorimetry to analyze the structural transitions of reflectins A1 and A2. We also analyzed the assembly behavior of phosphomimetic, deletion, and other mutants in conjunction with pH titration as an in vitro surrogate of phosphorylation. Our experiments uncovered a previously unsuspected, precisely predictive relationship between the extent of neutralization of a reflectin's net charge density and the size of resulting multimeric protein assemblies of narrow polydispersity. Comparisons of mutants revealed that this sensitivity to neutralization resides in the linkers and is spatially distributed along the protein. Imaging of large particles and analysis of sequence composition suggested that assembly may proceed through a dynamically arrested liquid-liquid phase-separated intermediate. Intriguingly, it is this dynamic arrest that enables the observed fine-tuning by charge and the resulting calibration between neuronal trigger and color in the squid. These results offer insights into the basis of reflectin-based biophotonics, opening paths for the design of new materials with tunable properties.

Ecological pressures and the contrasting scaling of metabolism and body shape in coexisting taxa: cephalopods versus teleost fish.

Metabolic rates are fundamental to many biological processes, and commonly scale with body size with an exponent ( bR) between 2/3 and 1 for reasons still debated. According to the 'metabolic-level boundaries hypothesis', bR depends on the metabolic level ( LR). We test this prediction and show that across cephalopod species intraspecific bR correlates positively with not only LR but also the scaling of body surface area with body mass. Cephalopod species with high LR maintain near constant mass-specific metabolic rates, growth and probably inner-mantle surface area for exchange of respiratory gases or wastes throughout their lives. By contrast, teleost fish show a negative correlation between bR and LR. We hypothesize that this striking taxonomic difference arises because both resource supply and demand scale differently in fish and cephalopods, as a result of contrasting mortality and energetic pressures, likely related to different locomotion costs and predation pressure. Cephalopods with high LR exhibit relatively steep scaling of growth, locomotion, and resource-exchange surface area, made possible by body-shape shifting. We suggest that differences in lifestyle, growth and body shape with changing water depth may be useful for predicting contrasting metabolic scaling for coexisting animals of similar sizes. This article is part of the theme issue 'Physiological diversity, biodiversity patterns and global climate change: testing key hypotheses involving temperature and oxygen'.

Laser imaging polarimetry of nacre.

Nacre is a complex biomaterial made of aragonite-tablet bricks and organic mortar that is considerably resilient against breakage. Nacre has been studied with a wide range of laboratory techniques, leading to understanding key fundamentals and informing the creation of bio-inspired materials. In this article, we present an optical polarimetric technique to investigate nacre, taking advantage of the translucence and birefringence of its microcomponents. We focus our study on 3 classes of mollusks that have nacreous shells: bivalve (Pinctada fucata), gastropod (Haliotis asinina and Haliotis rufescens) and cephalopod (Nautilus pompilius). We sent polarized light from a laser through thin samples of nacre and did imaging polarimetry of the transmitted light. We observed clear distinctions between the structures of bivalve and gastropod, due to the spatial variation of their birefringence. The patterns for cephalopod were more similar to bivalve than gastropod. Bleaching of the samples disrupted the transmitted light. Subsequent refilling of the bivalve and gastropod nacre samples with oil produced optical patterns similar to those of unbleached samples. In cephalopod samples, we found that bleaching produced irreversible changes in the optical pattern.

Trade-off between Transcriptome Plasticity and Genome Evolution in Cephalopods.

RNA editing, a post-transcriptional process, allows the diversification of proteomes beyond the genomic blueprint; however it is infrequently used among animals for this purpose. Recent reports suggesting increased levels of RNA editing in squids thus raise the question of the nature and effects of these events. We here show that RNA editing is particularly common in behaviorally sophisticated coleoid cephalopods, with tens of thousands of evolutionarily conserved sites. Editing is enriched in the nervous system, affecting molecules pertinent for excitability and neuronal morphology. The genomic sequence flanking editing sites is highly conserved, suggesting that the process confers a selective advantage. Due to the large number of sites, the surrounding conservation greatly reduces the number of mutations and genomic polymorphisms in protein-coding regions. This trade-off between genome evolution and transcriptome plasticity highlights the importance of RNA recoding as a strategy for diversifying proteins, particularly those associated with neural function. PAPERCLIP.

Metal bioaccumulation and detoxification processes in cephalopods: A review.

In recent decades, cephalopods have been shown to have very high capacities to accumulate most trace elements, regardless of whether they are essential (e.g., Cu and Zn) or non-essential (e.g., Ag and Cd). Among the different pathways of exposure to trace elements, the trophic pathway appears to be the major route of assimilation for numerous metals, including Cd, Co, Hg and Zn. Once assimilated, trace elements are distributed in the organism, accumulating in storage organs. The digestive gland is the main organ in which many trace elements accumulate, whichever of the exposure pathway. For example, this organ can present Cd concentrations reaching hundreds to thousands of ppm for some species, even though the digestive gland represents only a small proportion of the total mass of the animal. Such a specific organotropism towards the digestive gland of both essential and non-essential elements, regardless of the exposure pathway, poses the question of the detoxification processes evolved by cephalopods in order to sustain these high concentrations. This paper reviews the current knowledge on the bioaccumulation of trace elements in cephalopods, the differences in pharmaco-dynamics between organs and tissues, and the detoxification processes they use to counteract trace element toxicity. A peculiar focus has been done on the bioaccumulation within the digestive gland by investigating the subcellular locations of trace elements and their protein ligands.

Metal bioaccumulation in two edible cephalopods in the Gulf of Gabes, South-Eastern Tunisia: environmental and human health risk assessment.

Samples of Octopus vulgaris and Sepia officinalis were collected from four areas in the Gulf of Gabes, south-eastern Tunisia, and their edible tissues (mantle and arms) were analyzed for cadmium, copper, mercury, and zinc. While the concentrations of metals showed significant differences between the sampling sites, no differences were revealed between the tissues of the two species. The spatial distribution of metals analyzed showed similar pattern for both tissues of the two species, with the highest concentrations found in the central area of Gabes Gulf, and the lowest in the northern and/or southern areas. From a human health risk point of view, the highest values of estimated daily intake, target hazard quotient, and hazard index were found in the central area of Gabes Gulf. Although the results of these indices were, in general, not alarming, the health risks posed by the consumption of cephalopods on local consumers cannot be excluded.