Splice variants of perlucin from Haliotis laevigata modulate the crystallisation of CaCO3

Assessing marine ecosystem health using multi-omic analysis of blue mussel liquid biopsies: A case study within a national marine park

Marine ecosystems are under escalating threats from myriad environmental stressors, necessitating a deeper understanding of their impact on biodiversity and the health of sentinel organisms. In this study, we carried out a spatiotemporal multi-omic analysis of liquid biopsies collected from mussels (Mytilus spp.) in marine ecosystems of a national park. We delved into the epigenomic, transcriptomic, glycomic, proteomic, and microbiomic profiles to unravel the intricate interplay between ecosystem biodiversity and mussels' biological response to their environments. Our analysis revealed temporal fluctuations in the alpha diversity of the circulating microbiome associated with human activities. Analysis of the hemolymphatic circulating cell-free DNA (ccfDNA) provided information on the biodiversity and the presence of potential pathogens. Epigenomic analysis revealed widespread hypomethylation sites within the mitochondrial (mtDNA). Comparative transcriptomic and glycomic analyses highlighted differences in metabolic pathways and genes associated with immune and wound healing functions. This study demonstrates the potential of multi-omic analysis of liquid biopsy in sentinel to provide a holistic view of human activities' environmental impacts on marine coastal ecosystems. Overall, this approach has the potential to enhance the effectiveness and efficiency of various conservation efforts, leading to more informed decision-making and better outcomes for biodiversity and ecosystem conservation.

RNAi Silencing of the Biomineralization Gene Perlucin Impairs Oyster Ability to Cope with Ocean Acidification

Calcifying marine organisms, including the eastern oyster (Crassostrea virginica), are vulnerable to ocean acidification (OA) because it is more difficult to precipitate calcium carbonate (CaCO₃). Previous investigations of the molecular mechanisms associated with resilience to OA in C. virginica demonstrated significant differences in single nucleotide polymorphism and gene expression profiles among oysters reared under ambient and OA conditions. Converged evidence generated by both of these approaches highlighted the role of genes related to biomineralization, including perlucins. Here, gene silencing via RNA interference (RNAi) was used to evaluate the protective role of a perlucin gene under OA stress. Larvae were exposed to short dicer-substrate small interfering RNA (DsiRNA-perlucin) to silence the target gene or to one of two control treatments (control DsiRNA or seawater) before cultivation under OA (pH ~7.3) or ambient (pH ~8.2) conditions. Two transfection experiments were performed in parallel, one during fertilization and one during early larval development (6 h post-fertilization), before larval viability, size, development, and shell mineralization were monitored. Silenced oysters under acidification stress were the smallest, had shell abnormalities, and had significantly reduced shell mineralization, thereby suggesting that perlucin significantly helps larvae mitigate the effects of OA.

Brachiopod and mollusc biomineralisation is a conserved process that was lost in the phoronid-bryozoan stem lineage

BACKGROUND

Brachiopods and molluscs are lophotrochozoans with hard external shells which are often believed to have evolved convergently. While palaeontological data indicate that both groups are descended from biomineralising Cambrian ancestors, the closest relatives of brachiopods, phoronids and bryozoans, are mineralised to a much lower extent and are comparatively poorly represented in the Palaeozoic fossil record. Although brachiopod and mollusc shells are structurally analogous, genomic and proteomic evidence indicates that their formation involves a complement of conserved, orthologous genes. Here, we study a set of genes comprised of 3 homeodomain transcription factors, one signalling molecule and 6 structural proteins which are implicated in mollusc and brachiopod shell formation, search for their orthologs in transcriptomes or genomes of brachiopods, phoronids and bryozoans, and present expression patterns of 8 of the genes in postmetamorphic juveniles of the rhynchonelliform brachiopod T. transversa.

RESULTS

Transcriptome and genome searches for the 10 target genes in the brachiopods Terebratalia transversa, Lingula anatina, Novocrania anomala, the bryozoans Bugula neritina and Membranipora membranacea, and the phoronids Phoronis australis and Phoronopsis harmeri resulted in the recovery of orthologs of the majority of the genes in all taxa. While the full complement of genes was present in all brachiopods with a single exception in L. anatina, a bloc of four genes could consistently not be retrieved from bryozoans and phoronids. The genes engrailed, distal-less, ferritin, perlucin, sp1 and sp2 were shown to be expressed in the biomineralising mantle margin of T. transversa juveniles.

CONCLUSIONS

The gene expression patterns we recovered indicate that while mineralised shells in brachiopods and molluscs are structurally analogous, their formation builds on a homologous process that involves a conserved complement of orthologous genes. Losses of some of the genes related to biomineralisation in bryozoans and phoronids indicate that loss of the capacity to form mineralised structures occurred already in the phoronid-bryozoan stem group and supports the idea that mineralised skeletons evolved secondarily in some of the bryozoan subclades.

Modification of Surfaces with Vaterite CaCO3 Particles

Former studies have demonstrated a strong interest toward the crystallization of CaCO₃ polymorphs in solution. Nowadays, CaCO₃ crystallization on solid surfaces is extensively being studied using biomolecules as substrates for the control of the growth aiming at various applications of CaCO₃. Calcium carbonate exists in an amorphous state, as three anhydrous polymorphs (aragonite, calcite and vaterite), and as two hydrated polymorphs (monohydrocalcite and ikaite). The vaterite polymorph is considered as one of the most attractive forms due to its large surface area, biocompatibility, mesoporous nature, and other features. Based on physical or chemical immobilization approaches, vaterite can be grown directly on solid surfaces using various (bio)molecules, including synthetic polymers, biomacromolecules such as proteins and peptides, carbohydrates, fibers, extracellular matrix components, and even biological cells such as bacteria. Herein, the progress on the modification of solid surfaces by vaterite CaCO₃ crystals is reviewed, focusing on main findings and the mechanism of vaterite growth initiated by various substances mentioned above, as well as the discussion of the applications of such modified surfaces.

De novo transcriptome assembly of the midgut glands of herbivorous land crabs, Chiromantes haematocheir, and identification of laccase genes involved in lignin degradation

Herbivorous land crabs such as Chiromantes haematocheir and C. dehaani show biomass-degrading activities. In this study, we performed RNA-seq analysis to detect biomass-degrading enzymes. A de novo transcriptome assembly in the midgut glands of molting and non-molting C. haematocheir crabs was constructed using RNA sequencing. Illumina sequencing generated 44,937,002 and 44,394,310 reads from the two midgut glands. In total, 178,710 contigs with an average length of 750 bp and an N50 value of 1,235 bp were assembled, of which 37,890 contigs were annotated using BLASTx search against the NCBI database. We identified 22 contigs (11 genes) belonging to the laccase family and 44 contigs (22 genes) belonging to the peroxidase family. Sixteen contigs (three genes) belonging to the GH9 cellulase family were also detected. We selected the gene accounting for the majority of expressed laccase and analyzed its properties. The 24131-laccase transcript (2465 bp) had one complete open reading frame, nt 149-1987, encoding a protein of 613 amino acids with a deduced molecular mass of 67.708 kDa. The enzyme was shown to belong to the multicopper oxidase family. The 24131-laccase protein was confirmed to have oxidation activity against 2,6-dimethoxyphenol by ectopic expression in Escherichia coli. Laccase activity was significantly enhanced by feeding land crabs with plant diets. These data suggest that the enzyme plays an important role in the digestion of lignin in the guts of land crabs.

The protein and volatile components of trail mucus in the Common Garden Snail, Cornu aspersum

The Common or Brown Garden Snail, Cornu aspersum, is an invasive land snail that has successfully colonized a diverse range of global environments. Like other invasive land snails, it is a significant pest of a variety of agricultural crops, including citrus, grapes and canola. Cornu aspersum secretes a mucus trail when mobile that facilitates locomotion. The involvement of the trail in conspecific chemical communication has also been postulated. Our study found that anterior tentacle contact with conspecific mucus elicited a significant increase in heart rate from 46.9 to 51 beats per minute. In order to gain a better understanding of the constituents of the trail mucus and the role it may play in snail communication, the protein and volatile components of mucus trails were investigated. Using two different protein extraction methods, mass spectrometry analysis yielded 175 different proteins, 29 of which had no significant similarity to any entries in the non-redundant protein sequence database. Of the mucus proteins, 22 contain features consistent with secreted proteins, including a perlucin-like protein. The eight most abundant volatiles detected using gas chromatography were recorded (including propanoic acid and limonene) and their potential role as putative pheromones are discussed. In summary, this study has provided an avenue for further research pertaining to the role of trail mucus in snail communication and provides a useful repository for land snail trail mucus components. This may be utilized for further research regarding snail attraction and dispersal, which may be applied in the fields of agriculture, ecology and human health.

Acidification stress effect on umbonate veliger larval development in Panopea globosa

Ocean acidification generates a decrease in calcium carbonate availability essential for biomineralization in organisms such as mollusks. This effect was evaluated on Panopea globosa exposing for 7 days umbonate veliger larvae to two pH treatments: experimental (pH 7.5) and control (pH 8.0). Exposure to pH 7.5 affected growth, reducing larval shell length from 5.15-13.34% compared to the control group. This size reduction was confirmed with electron microscopy, also showing shell damage. The physiological response showed an increase in oxygen consumption in larvae exposed to low pH with a maximum difference of 1.57 nmol O₂ h^-1 larvae^-1 at day 7. The gene expression analyses reported high expression values for nicotinamide adenine dinucleotide (NADH) dehydrogenase and Perlucin in larvae at pH 7.5, suggesting a higher energetic cost in this larval group to maintain homeostasis. In conclusion, this study showed that acidification affected development of P. globosa umbonate veliger larvae.

A typical C-type lectin, perlucin-like protein, is involved in the innate immune defense of whiteleg shrimp Litopenaeus vannamei

C-type lectins are a large group of the pattern-recognition proteins, and have been reported to be involved in invertebrate innate immunity, such as cell adhesion, bacterial clearance, phagocytosis, prophenoloxidase activation and encapsulation. Here, a perlucin-like protein (PLP), a typical C-type lectin, was identified from the cDNA library of the shrimp, Litopenaeus vannamei. LvPLP contains a 540 bp open reading frame, encoding a protein of 179 amino acids that includes a single carbohydrate-recognition domain. Phylogenetic analysis showed that LvPLP was clustered into a single group together with other perlucins from molluscs. Quantitative real-time PCR revealed that LvPLP was expressed mainly in the hemocytes, hemolymph, heart and gills. The transcription of LvPLP was significantly induced at 9 h by both Gram^- bacteria Vibrio parahaemolyticus and Vibrio anguillarum. Meanwhile, recombinant LvPLP (rLvPLP) bound directly to lipopolysaccharide and peptidoglycan with different affinity. rLvPLP showed a strong ability to bind to Gram⁺ (Staphylococcus aureus and Bacillus subtilis) and Gram^- bacteria (V. parahaemolyticus and V. anguillarum), and could induce agglutination of V. parahaemolyticus and V. anguillarum, but not S. aureus and B. subtilis in the presence Ca²⁺. Further study showed that when LvPLP was knocked down by RNAi, three phagocytosis-related genes (peroxinectin, mas-like protein and dynamin) and four antimicrobial peptide (AMP) genes (crustin, ALF1, ALF2 and ALF3) were significantly decreased. Altogether, these results demonstrated that LvPLP played a vital role in L. vannamei immune response towards bacterial challenge by binding and agglutinating bacteria and influencing phagocytosis and AMP expression.

Glycan Binding Profiling of Jacalin-Related Lectins from the Pteria Penguin Pearl Shell

We determined the primary structures of jacalin-related lectins termed PPL3s (PPL3A, 3B, and 3C, which are dimers consisting of sequence variants α + α, α + β, β + β, respectively) and PPL4, which is heterodimer consisting of α + β subunits, isolated from mantle secretory fluid of Pteria penguin (Mabe) pearl shell. Their carbohydrate-binding properties were analyzed, in addition to that of PPL2A, which was previously reported as a matrix protein. PPL3s and PPL4 shared only 35–50% homology to PPL2A, respectively; they exhibited significantly different carbohydrate-binding specificities based on the multiple glycan binding profiling data sets from frontal affinity chromatography analysis. The carbohydrate-binding specificity of PPL3s was similar to that of PPL2A, except only for Man₃Fuc₁Xyl₁GlcNAc₂ oligosaccharide, while PPL4 showed different carbohydrate-binding specificity compared with PPL2A and PPL3s. PPL2A and PPL3s mainly recognize agalactosylated- and galactosylated-type glycans. On the other hand, PPL4 binds to high-mannose-and hybrid-type N-linked glycans but not agalactosylated- and galactosylated-type glycans.

The Molecular Differentiation of Anatomically Paired Left and Right Mantles of the Pacific Oyster Crassostrea gigas

Left-right (L-R) asymmetry is controlled by gene regulation pathways for the L-R axis, and in vertebrates, the gene Pitx2 in TGF-β signaling pathway plays important roles in the asymmetrical formation of organs. However, less is known about the asymmetries of anatomically identical paired organs, as well as the transcriptional regulation mechanism of the gene Pitx in invertebrates. Here, we report the molecular biological differences between the left and right mantles of an invertebrate, the Pacific oyster Crassostrea gigas, and propose one possible mechanism underlying those differences. RNA sequencing (RNA-seq) analysis indicated that the paired organs showed different gene expression patterns, suggesting possible functional differences in shell formation, pheromone signaling, nerve conduction, the stress response, and other physiological processes. RNA-seq and real-time qPCR analysis indicated high right-side expression of the Pitx homolog (cgPitx) in oyster mantle, supporting a conserved role for Pitx in controlling asymmetry. Methylation-dependent restriction-site associated DNA sequencing (MethylRAD) identified a methylation site in the promoter region of cgPitx and showed significantly different methylation levels between the left and right mantles. This is the first report, to our knowledge, of such a difference in methylation in spiralians, and it was further confirmed in 18 other individuals by using a pyrosequencing assay. The miRNome analysis and the TGF-β receptor/Smad inhibition experiment further supported that several genes in TGF-β signaling pathway may be related with the L/R asymmetry of oyster mantles. These results suggested that the molecular differentiation of the oyster's paired left and right mantles is significant, TGF-β signaling pathway could be involved in establishing or maintaining the asymmetry, and the cgPitx gene as one of genes in this pathway; the different methylation levels in its promoter regions between L/R mantles was the one of possible mechanisms regulating the left-right functional differentiation.

In-depth proteomic analyses of Haliotis laevigata (greenlip abalone) nacre and prismatic organic shell matrix

Background

The shells of various Haliotis species have served as models of invertebrate biomineralization and physical shell properties for more than 20 years. A focus of this research has been the nacreous inner layer of the shell with its conspicuous arrangement of aragonite platelets, resembling in cross-section a brick-and-mortar wall. In comparison, the outer, less stable, calcitic prismatic layer has received much less attention. One of the first molluscan shell proteins to be characterized at the molecular level was Lustrin A, a component of the nacreous organic matrix of Haliotis rufescens. This was soon followed by the C-type lectin perlucin and the growth factor-binding perlustrin, both isolated from H. laevigata nacre, and the crystal growth-modulating AP7 and AP24, isolated from H. rufescens nacre. Mass spectrometry-based proteomics was subsequently applied to to Haliotis biomineralization research with the analysis of the H. asinina shell matrix and yielded 14 different shell-associated proteins. That study was the most comprehensive for a Haliotis species to date.

Methods

The shell proteomes of nacre and prismatic layer of the marine gastropod Haliotis laevigata were analyzed combining mass spectrometry-based proteomics and next generation sequencing.

Results

We identified 297 proteins from the nacreous shell layer and 350 proteins from the prismatic shell layer from the green lip abalone H. laevigata. Considering the overlap between the two sets we identified a total of 448 proteins. Fifty-one nacre proteins and 43 prismatic layer proteins were defined as major proteins based on their abundance at more than 0.2% of the total. The remaining proteins occurred at low abundance and may not play any significant role in shell fabrication. The overlap of major proteins between the two shell layers was 17, amounting to a total of 77 major proteins.

Conclusions

The H. laevigata shell proteome shares moderate sequence similarity at the protein level with other gastropod, bivalve and more distantly related invertebrate biomineralising proteomes. Features conserved in H. laevigata and other molluscan shell proteomes include short repetitive sequences of low complexity predicted to lack intrinsic three-dimensional structure, and domains such as tyrosinase, chitin-binding, and carbonic anhydrase. This catalogue of H. laevigata shell proteins represents the most comprehensive for a haliotid and should support future efforts to elucidate the molecular mechanisms of shell assembly.

Electronic supplementary material

The online version of this article (10.1186/s12953-018-0139-3) contains supplementary material, which is available to authorized users.

Organic Filling Mitigates Flaw-Sensitivity of Nanoscale Aragonite

Engineering at nanoscale holds the promise of tuning materials with extraordinary properties. However, macroscopic approaches commonly used to predict mechanical properties do not fully apply at nanoscale level. A controversial feature is the presence of nanoflaws in aragonite nacre, as it is expected that flaws would weaken the material, whereas nacre still shows high toughness and rupture strength. Here, we performed molecular dynamics and finite element simulations emulating flaws found in aragonite nacre. Our simulations reveal two regimes for fracture: nacre remains flaw-insensitive only for flaws smaller than 1.2 nm depth, or flaws of a few atoms, whereas larger flaws follow a Griffith-like trend resembling macroscopic fracture. We tested an alternative mechanism for flaw-insensitivity in nacre, and investigated the mechanical effect of organic filling to mitigate fracture. We found that a single nacre protein, perlucin, decreases the stress concentration at the fracture point, producing enhancements of up to 15% in rupture strength. Our study reveals a more comprehensive understanding of mechanical stability at the nanoscale and offers new routes toward hybrid nanomaterials.

Intrinsically disordered proteins and biomineralization

In vertebrates and invertebrates, biomineralization is controlled by the cell and the proteins they produce. A large number of these proteins are intrinsically disordered, gaining some secondary structure when they interact with their binding partners. These partners include the component ions of the mineral being deposited, the crystals themselves, the template on which the initial crystals form, and other intrinsically disordered proteins and peptides. This review speculates why intrinsically disordered proteins are so important for biomineralization, providing illustrations from the SIBLING (small integrin binding N-glycosylated) proteins and their peptides. It is concluded that the flexible structure, and the ability of the intrinsically disordered proteins to bind to a multitude of surfaces is crucial, but details on the precise-interactions, energetics and kinetics of binding remain to be determined.

Crystallization of calcium carbonate under the influences of casein and magnesium ions

The significant morphological changes of calcium carbonate crystals were investigated and observed in the presence of casein and magnesium ions.

Natural Composite Systems for Bioinspired Materials

From a relatively limited selection of base materials, nature has steered the development of truly remarkable materials. The simplest and often overlooked organisms have demonstrated the ability to manufacture multi-faceted, molecular-level hierarchical structures that combine mechanical properties rarely seen in synthetic materials. Indeed, these natural composite systems, composed of an array of intricately arranged and functionally relevant organic and inorganic substances serve as inspiration for materials design. A better understanding of these composite systems, specifically at the interface of the hetero-assemblies, would encourage faster development of environmentally friendly "green" materials with molecular level specificities.

A bio-process inspired synthesis of vaterite (CaCO3), directed by a rationally designed multifunctional protein, ChiCaSifi

A bio-process inspired synthesis of vaterite (CaCO₃) is achieved under the functions of a rationally designed multifunctional protein, ChiCaSifi.