The molecular mechanism of calcification in aquatic organisms

Identification of Candidate Male-Reproduction-Related Genes from the Testis and Androgenic Gland of Macrobrachium nipponense, Regulated by PDHE1, through Transcriptome Profiling Analysis

The previous publication identified that pyruvate dehydrogenase E1 (PDHE1) positively regulated the process of male reproduction in M. nipponense through affecting the expressions of insulin-like androgenic gland hormone. The present study aimed to identify the potential male-reproduction-related genes that were regulated by PDHE1 through performing the transcriptome profiling analysis in the testis and androgenic gland after the knockdown of the expressions of PDHE1 by the injection of dsPDHE1. Both RNA-Seq and qPCR analysis identified the significant decreases in PDHE1 expressions in the testis and androgenic gland in dsPDHE1-injected prawns compared to those in dsGFP-injected prawns, indicating the efficiency of dsPDHE1 in the present study. Transcriptome profiling analysis identified 56 and 127 differentially expressed genes (DEGs) in the testis and androgenic gland, respectively. KEGG analysis revealed that the energy-metabolism-related pathways represented the main enriched metabolic pathways of DEGs in both the testis and androgenic gland, including pyruvate metabolism, the Citrate cycle (TCA cycle), Glycolysis/Gluconeogenesis, and the Glucagon signaling pathway. Thus, it is predicted that these metabolic pathways and the DEGs from these metabolic pathways regulated by PDHE1 may be involved in the regulation of male reproduction in M. nipponense. Furthermore, four genes were found to be differentially expressed in both the testis and androgenic gland, of which ribosomal protein S3 was down-regulated and uncharacterized protein LOC113829596 was up-regulated in both the testis and androgenic gland in dsPDHE1-injected prawns. The present study provided valuable evidence for the establishment of an artificial technique to regulate the process of male reproduction in M. nipponense.

Spatial distributions of and species differences in 90Sr accumulation in marine fishes from the Fukushima coastal region

Large amounts of radionuclides were released into the ocean during the Fukushima Dai-ichi Nuclear Power Plant (FDNPP) accident. One of the released radionuclides, 90Sr, tends to accumulate in bone, and could conceivably have long-term negative impacts on fishes. Here, we investigated 90Sr radioactivity concentrations in the vertebrae of demersal fishes collected off the coast of Fukushima Prefecture in January and July 2014. High 90Sr radioactivity concentrations were detected in fish collected from central Fukushima (offshore of the FDNPP) and southern Fukushima (offshore of Iwaki City), but were almost hardly detected in northern Fukushima (offshore of Soma City). Additionally, 90Sr radioactivity concentrations were higher among rays (Okamejei kenojei and Hemitrygon akajei: from 1.1 ± 0.5 to 103.3 ± 15.1 mBq/g Ca) and soles (Cynoglossus joyneri and Paraplagusia japonica: from 18.5 ± 2.8 to 52.8 ± 11.3 mBq/g Ca) than among other species. Vertebral stable Sr/Ca ratios also differed by fish species. Ca concentrations were relatively constant among species, but Sr concentrations were higher among elasmobranchs and soles, indicating that differences in Sr/Ca might be related to differences in 90Sr accumulation in fish vertebrae.

Influence of ontogenetic development, temperature, and pCO2 on otolith calcium carbonate polymorph composition in sturgeons

Changes to calcium carbonate (CaCO₃) biomineralization in aquatic organisms is among the many predicted effects of climate change. Because otolith (hearing/orientation structures in fish) CaCO₃ precipitation and polymorph composition are controlled by genetic and environmental factors, climate change may be predicted to affect the phenotypic plasticity of otoliths. We examined precipitation of otolith polymorphs (aragonite, vaterite, calcite) during early life history in two species of sturgeon, Lake Sturgeon, (Acipenser fulvescens) and White Sturgeon (A. transmontanus), using quantitative X-ray microdiffraction. Both species showed similar fluctuations in otolith polymorphs with a significant shift in the proportions of vaterite and aragonite in sagittal otoliths coinciding with the transition to fully exogenous feeding. We also examined the effect of the environment on otolith morphology and polymorph composition during early life history in Lake Sturgeon larvae reared in varying temperature (16/22 °C) and pCO₂ (1000/2500 µatm) environments for 5 months. Fish raised in elevated temperature had significantly increased otolith size and precipitation of large single calcite crystals. Interestingly, pCO₂ had no statistically significant effect on size or polymorph composition of otoliths despite blood pH exhibiting a mild alkalosis, which is contrary to what has been observed in several studies on marine fishes. These results suggest climate change may influence otolith polymorph composition during early life history in Lake Sturgeon.

Identification of methionine -rich insoluble proteins in the shell of the pearl oyster, Pinctada fucata

The molluscan shell is a biomineral that comprises calcium carbonate and organic matrices controlling the crystal growth of calcium carbonate. The main components of organic matrices are insoluble chitin and proteins. Various kinds of proteins have been identified by solubilizing them with reagents, such as acid or detergent. However, insoluble proteins remained due to the formation of a solid complex with chitin. Herein, we identified these proteins from the nacreous layer, prismatic layer, and hinge ligament of Pinctada fucata using mercaptoethanol and trypsin. Most identified proteins contained a methionine-rich region in common. We focused on one of these proteins, NU-5, to examine the function in shell formation. Gene expression analysis of NU-5 showed that NU-5 was highly expressed in the mantle, and a knockdown of NU-5 prevented the formation of aragonite tablets in the nacre, which suggested that NU-5 was required for nacre formation. Dynamic light scattering and circular dichroism revealed that recombinant NU-5 had aggregation activity and changed its secondary structure in the presence of calcium ions. These findings suggest that insoluble proteins containing methionine-rich regions may be important for scaffold formation, which is an initial stage of biomineral formation.

Functional shell matrix proteins tentatively identified by asymmetric snail shell morphology

Molluscan shell matrix proteins (SMPs) are essential in biomineralization. Here, we identify potentially important SMPs by exploiting the asymmetric shell growth in snail, Lymnaea stagnalis. Asymmetric shells require bilaterally asymmetric expression of SMP genes. We examined expression levels of 35,951 transcripts expressed in the left and right sides of mantle tissue of the pond snail, Lymnaea stagnalis. This transcriptome dataset was used to identify 207 SMPs by LC-MS/MS. 32 of the 207 SMP genes show asymmetric expression patterns, which were further verified for 4 of the 32 SMPs using quantitative PCR analysis. Among asymmetrically expressed SMPs in dextral snails, those that are more highly expressed on the left side than the right side are 3 times more abundant than those that are more highly expressed on the right than the left, suggesting potentially inhibitory roles of SMPs in shell formation. The 32 SMPs thus identified have distinctive features, such as conserved domains and low complexity regions, which may be essential in biomineralization.

Blueprints for the Next Generation of Bioinspired and Biomimetic Mineralised Composites for Bone Regeneration

Coccolithophores are unicellular marine phytoplankton, which produce intricate, tightly regulated, exoskeleton calcite structures. The formation of biogenic calcite occurs either intracellularly, forming ‘wheel-like’ calcite plates, or extracellularly, forming ‘tiled-like’ plates known as coccoliths. Secreted coccoliths then self-assemble into multiple layers to form the coccosphere, creating a protective wall around the organism. The cell wall hosts a variety of unique species-specific inorganic morphologies that cannot be replicated synthetically. Although biomineralisation has been extensively studied, it is still not fully understood. It is becoming more apparent that biologically controlled mineralisation is still an elusive goal. A key question to address is how nature goes from basic building blocks to the ultrafine, highly organised structures found in coccolithophores. A better understanding of coccolithophore biomineralisation will offer new insight into biomimetic and bioinspired synthesis of advanced, functionalised materials for bone tissue regeneration. The purpose of this review is to spark new interest in biomineralisation and gain new insight into coccolithophores from a material science perspective, drawing on existing knowledge from taxonomists, geologists, palaeontologists and phycologists.

Fungal-type carbohydrate binding modules from the coccolithophore Emiliania huxleyi show binding affinity to cellulose and chitin

Six fungal-type cellulose binding domains were found in the genome of the coccolithophore Emiliania huxleyi and cloned and expressed in Escherichia coli. Sequence comparison indicate high similarity to fungal cellulose binding domains, raising the question of why these domains exist in coccolithophores. The proteins were tested for binding with cellulose and chitin as ligands, which resulted in the identification of two functional carbohydrate binding modules: EHUX2 and EHUX4. Compared to benchmark fungal cellulose binding domain Cel7A-CBM1 from Trichoderma reesei, these proteins showed slightly lower binding to birch and bacterial cellulose, but were more efficient chitin binders. Finally, a set of cellulose binding domains was created based on the shuffling of one well-functioning and one non-functional domain. These were characterized in order to get more information of the binding domain’s sequence–function relationship, indicating characteristic differences between the molecular basis of cellulose versus chitin recognition. As previous reports have showed the presence of cellulose in coccoliths and here we find functional cellulose binding modules, a possible connection is discussed.

Molecular cloning and functional analysis of chitinases in the fresh water snail, Lymnaea stagnalis

Molluscan shells, consisting of calcium carbonate, are typical examples of biominerals. The small amount of organic matrices containing chitin and proteins in molluscan shells regulates calcification to produce elaborate microstructures. The shells of gastropods have a spiral shape around a central axis. The shell thickness on the internal side of the spiral becomes thinner than that on the outer side of the spiral during the growth to expand the interior space. These observations suggest that a dissolution process works as a remodeling mechanism to change shell shape in molluscan shells. To reveal the dissolution mechanism involved in the remodeling of gastropod spiral shells, we focused on chitinases in the fresh water snail Lymnaea stagnalis. Chitinase activity was observed in the acetic acid-soluble fraction of the shell and in the buffer extract from the mantle. Allosamidin, a specific inhibitor of family 18 chitinases, inhibited the chitinase activity of both fractions completely. Homology cloning and transcriptome analyses of the mantle revealed five genes (chi-I, chi-II, chi-III, chi-IV, and chi-V) encoding family 18 chitinases. All chitinases were expressed in the mantle and in other tissues suggesting that chitinases in the mantle have multiple-functions. Treatment with commercially available chitinase obtained from Trichoderma viride altered the shell microstructure of L. stagnalis. Larvae of L. stagnalis cultured in allosamidin solution had a thinner organic layer on the shell surface. These results suggest that the chitinase activities in the shell and mantle are probably associated with the shell formation process.

Sagittal otolith morphogenesis asymmetry in marine fishes

This study investigated and compared asymmetry in sagittal otolith shape and length between left and right inner ears in four roundfish and four flatfish species of commercial interest. For each species, the effects of ontogenetic changes (individual age and total body length), sexual dimorphism (individual sex) and the otolith's location on the right or left side of the head, on the shape and length of paired otoliths (between 143 and 702 pairs according to species) were evaluated. Ontogenetic changes in otolith shape and length were observed for all species. Sexual dimorphism, either in otolith shape and length or in their ontogenetic changes, was detected for half of the species, be they round or flat. Significant directional asymmetry in otolith shape and length was detected in one roundfish species each, but its inconsistency across species and its small average amplitude (6·17% for shape and 1·99% for length) suggested that it has barely any biological relevance. Significant directional asymmetry in otolith shape and length was found for all flatfish species except otolith length for one species. Its average amplitude varied between 2·06 and 17·50% for shape and between 0·00 and 11·83% for length and increased significantly throughout ontogeny for two species, one dextral and one sinistral. The longer (length) and rounder otolith (shape) appeared to be always on the blind side whatever the species. These results suggest differential biomineralization between the blind and ocular inner ears in flatfish species that could result from perturbations of the proximal-distal gradient of otolith precursors in the endolymph and the otolith position relative to the geometry of the saccular epithelium due to body morphology asymmetry and lateralized behaviour. The fact that asymmetry never exceeded 18% even at the individual level suggests an evolutionary canalization of otolith shape symmetry to avoid negative effects on fish hearing and balance. Technically, asymmetry should be accounted for in future studies based on otolith shape.

Identification of ligament intra-crystalline peptide (LICP) from the hinge ligament of the bivalve, Pinctada fucata

The hinge ligament of the bivalve is an important hard tissue that functions to open and close the shells. The ligament contains a fibrous structure consisting of aragonite crystals surrounded by dense organic matrices. Although many matrix proteins have been identified from various shell microstructures in previous works, ligament-specific matrix proteins have not yet been reported. In this study, in order to reveal the formation mechanism of the fibrous aragonite crystals in the ligament of Pinctada fucata, we identified a novel, small acidic peptide, named ligament intra-crystalline peptide (LICP), from the aragonite crystal of the ligament that had been pre-treated with sodium hypochlorite to remove the inter-crystalline organic matrices. LICP consists of 10 amino acid residues with N-terminal pyroglutamic acid. The result of cDNA cloning showed that the cDNA encodes another putative 10-residue peptide at the C-terminal end of LICP. LICP showed inhibitory activity on calcium carbonate precipitation, while the synthetic 10-residue peptide from the C-terminal sequence of proLICP did not. We also noted that the TEM and SEM observations of aragonite crystals formed by the in vitro crystallization experiment showed that LICP inhibited the growth of aragonite crystal to stop elongation in the c-axis direction. These results suggested that LICP has a role of regulating the formation of the aragonite crystals in the ligament.

Unexpected link between polyketide synthase and calcium carbonate biomineralization

INTRODUCTION

Calcium carbonate biominerals participate in diverse physiological functions. Despite intensive studies, little is known about how mineralization is initiated in organisms.

RESULTS

We analyzed the medaka spontaneous mutant, ha, defective in otolith (calcareous ear stone) formation. ha lacks a trigger for otolith mineralization, and the causative gene was found to encode polyketide synthase (pks), a multifunctional enzyme mainly found in bacteria, fungi, and plant. Subsequent experiments demonstrate that the products of medaka PKS, most likely polyketides or their derivatives, act as nucleation facilitators in otolith mineralization. The generality of this novel PKS function is supported by the essential role of echinoderm PKS in calcareous skeleton formation together with the presence of PKSs in a much wider range of animals from coral to vertebrates.

CONCLUSION

The present study first links PKS to biomineralization and provides a genetic cue for biogeochemistry of carbon and calcium cycles.