Molecular cloning of the crustacean DD4 cDNA encoding a Ca(2+)-binding protein

Transcriptomic analysis reveals nanoplastics-induced apoptosis, autophagy and immune response in Litopenaeus vannamei

Increasing attention is being paid to the toxic physiological effects of nanoplastics (NPs) on aquatic organisms. However, few studies have systematically evaluated the regulatory mechanisms of NPs on immune response in crustaceans. In this study, a 28-day chronic exposure experiment was conducted in which shrimps were exposed to various 80-nm polystyrene NPs concentrations (0, 0.1, 1, 5 and 10 mg/L). Transcriptomic analysis was used to investigate the regulatory mechanisms of NPs in immune response of Litopenaeus vannamei. With increasing NPs concentration, the total hemocyte count (THC) content decreased, while phagocytosis rate (PR) and respiratory burst (RB) showed trends of first rising and then falling. High concentration (10 mg/L) of NPs caused the destruction of hepatopancreas tissue structure, the shedding of microvilli, the increase number of hepatocyte apoptosis and autophagy structure. With increasing NPs concentration, the lysozyme (Lys), superoxide dismutase (SOD) and glutathione peroxidase (GPx) activities first increased and then decrease, while contents of lipid peroxidation and malondialdehyde increased; the expression levels of Toll, MyD88, GPx, SOD, proPO, Lys, and ALF generally increased at first and then decreased. Transcriptional sequencing analysis showed that the pathway of differentially expressed genes in KEGG enrichment mainly included lysosome (ko04142), apoptosis (ko04210) pathways, indicating that the NPs mainly affected the immune regulatory mechanism. Further analysis by Gene Set Enrichment Analysis (GSEA) showed that the up-regulation pathways of NPs activation mainly included immune response-related pathways such as mitochondrial autophagy, DNA repair, autophagosomes signaling pathway. Our results indicated that NPs exposure induced oxidative stress, apoptosis and autophagy in shrimps. This study provides a basis for further understanding of the mechanisms of antioxidant immune regulation by NPs in shrimp and may serve as a reference for healthy ecological culture of shrimp.

Exoskeleton protein repertoires in decapod crustaceans revealed distinct biomineralization evolution with molluscs

Crustaceans are the champions of mineral mobilization and deposition in the animal kingdom due to their unique ability to rapidly and periodically mineralize and demineralize their exoskeletons. They are commonly covered with mineralized exoskeletons for protection and regularly molt throughout their lives. Mineralized crustacean exoskeletons are formed under the control of macromolecules especially matrix proteins but the types of matrix proteins are understudied compared to those in molluscan shells. This gap hinders our understanding of their evolutionary paths compared with those of molluscs. Here, we comprehensively analyzed matrix proteins in the exoskeleton of two crabs, one shrimp, and one crayfish and resulted in a major improvement (∼10-fold) in the identification of biomineralization proteins compared to conventional methods for decapod crustaceans. By a comparison with well-studied molluscan biomineralization proteins, we found that decapod crustaceans evolved novel proteins to form mineralized exoskeletons while sharing some proteins with those of molluscs. Our study sheds light on their evolution and adaption to different environment for exoskeleton formation and provides a foundation for further studies of mineralization in crustaceans under normal and climate-changed conditions. SIGNIFICANCE: Most crustaceans have mineralized exoskeletons as protection. How they form these hierarchical structures is still unclear. This is due partially to the understudied matrix proteins in the minerals. This study filled such a gap by using proteomic analysis of matrix proteins from four decapod crustacean exoskeletons. Many novel proteins were discovered which enabled a solid comparison with those of molluscs. By comparison, we proposed that crustaceans evolved novel proteins to form mineralized exoskeletons while sharing some proteins with those of molluscs. This is useful for us to understand the evolution of two major biomineralized phylum.

Probiotic Effects of a Marine Purple Non-Sulfur Bacterium, Rhodovulum sulfidophilum KKMI01, on Kuruma Shrimp (Marsupenaeus japonicus)

Purple non-sulfur bacteria (PNSB) are used as probiotics in shrimp aquaculture; however, no studies have examined the probiotic effects of PNSB in shrimp at the gene expression level. In this study, we examined the effects of a marine PNSB, Rhodovulum sulfidophilum KKMI01, on the gene expression of kuruma shrimp (Marsupenaeus japonicus). Short-term (3 days) effects of R. sulfidophilum KKMI01 on the gene expression in shrimp were examined using small-scale laboratory aquaria experiments, while long-term (145 days) effects of R. sulfidophilum KKMI01 on the growth performance and gene expression were examined using 200-ton outdoor aquaria experiments. Gene expression levels were examined using qRT-PCR. Results of the short-term experiments showed the upregulation of several molting-related genes, including cuticle proteins, calcification proteins, and cuticle pigment protein, suggesting that PNSB stimulated the growth of shrimp. The upregulation of several immune genes, such as prophenoloxidase, antimicrobial peptides, and superoxide dismutase, was also observed. In the 145-day outdoor experiments, the average body weight at harvest time, survival rate, and feed conversion ratio were significantly improved in PNSB-treated shrimp, and upregulation of molting and immune-related genes were also observed. When PNSB cells were added to the rearing water, the effective dosage of PNSB was as low as 10³ cfu/mL, which was more than a million times dilution of the original PNSB culture (2–3 × 10⁹ cfu/mL), indicating that R. sulfidophilum KKMI01 provides a feasible and cost-effective application as a probiotic candidate in shrimp aquaculture.

PmCBP, a novel poly (chitin-binding domain) gene, participates in nacreous layer formation of Pinctada fucata martensii

Chitin participates in shell formation as the main component of an organic framework. Chitin-binding protein contains domains that can bind to chitin specifically. In this study, a novel chitin-binding protein from Pinctada fucata martensii (PmCBP) with poly (chitin-binding domain) was cloned, which contains a 5'-untranslated region (UTR) of 114 bp and 3'UTR of 116 bp, and encodes a putative protein of 2044 amino acids. The predicted PmCBP protein was structurally typical of the CBP family with 20 ChtBD2 domains. Phylogenetic and linear relation analyses showed that the ChtBD2 domain has a highly conserved structure among the three species of P. f. martensii, Crassostrea gigas, and Mizuhopecten yessoensis. qRT-PCR and in-situ hybridization analysis revealed that PmCBP was most abundant in the mantle pallium whose expression level was significantly correlated with the growth traits. After RNAi, PmCBP expression was significantly inhibited in the mantle pallium (P < 0.05) and the microstructure of nacreous layers showed a disordered growth in the experiment group. These results indicated that PmCBP may be involved in nacreous layer formation through participation in the process of binding chitin in pearl oyster P. f. martensii.

Hichin, a chitin binding protein is essential for the self-assembly of organic frameworks and calcium carbonate during shell formation

Shell biomineralization is a process where inorganic minerals accumulate upon a chitinous scaffold under the control of multifunctional matrix proteins. In this study, we cloned a novel matrix protein gene from the mantle of Hyriopsis cumingii. The predicted protein, hichin, contains a chitin-binding domain and exhibited the highest expressional level in mantle tissue, with positive signals mainly detected in dorsal epithelial cells of the pallial mantle according to in situ hybridization, indicating its possible involvement in shell nacreous layer biomineralization. RNA interference showed that hichin suppression induced disordered self-assembly of the insoluble framework in the nacreous layer, and that the newly formed calcium carbonate crystals could not bind to organic frameworks. Furthermore, hichin was primarily responsible for building the framework during initial nacre deposition in pearl formation. Moreover, the chitin-binding domain of hichin also provided crystal morphology regulation in vitro crystallization assay. These results indicated that hichin is involved in the self-assembly of organic frameworks and morphological regulation in shell nacreous layer.

Compartmentalization and Ca2+ buffering are essential for prevention of light-induced retinal degeneration

Fly photoreceptors are polarized cells, each of which has an extended interface between its cell body and the light-signaling compartment, the rhabdomere. Upon intense illumination, rhabdomeric calcium concentration reaches millimolar levels that would be toxic if Ca(2+) diffusion between the rhabdomere and cell body was not robustly attenuated. Yet, it is not clear how such effective attenuation is obtained. Here we show that Ca(2+) homeostasis in the photoreceptor cell relies on the protein calphotin. This unique protein functions as an immobile Ca(2+) buffer localized along the base of the rhabdomere, separating the signaling compartment from the cell body. Generation and analyses of transgenic Drosophila strains, in which calphotin-expression levels were reduced in a graded manner, showed that moderately reduced calphotin expression impaired Ca(2+) homeostasis while calphotin elimination resulted in severe light-dependent photoreceptor degeneration. Electron microscopy, electrophysiology, and optical methods revealed that the degeneration was rescued by prevention of Ca(2+) overload via overexpression of CalX, the Na(+)-Ca(2+) exchanger. In addition, Ca(2+)-imaging experiments showed that reduced calphotin levels resulted in abnormally fast kinetics of Ca(2+) elevation in photoreceptor cells. Together, the data suggest that calphotin functions as a Ca(2+) buffer; a possibility that we directly demonstrate by expressing calphotin in a heterologous expression system. We propose that calphotin-mediated compartmentalization and Ca(2+) buffering constitute an effective strategy to protect cells from Ca(2+) overload and light-induced degeneration.

Biomineralizations: insights and prospects from crustaceans

For growing, crustaceans have to molt cyclically because of the presence of a rigid exoskeleton. Most of the crustaceans harden their cuticle not only by sclerotization, like all the arthropods, but also by calcification. All the physiology of crustaceans, including the calcification process, is then linked to molting cycles. This means for these animals to find regularly a source of calcium ions quickly available just after ecdysis. The sources of calcium used are diverse, ranging from the environment where the animals live to endogenous calcium deposits cyclically elaborated by some of them. As a result, crustaceans are submitted to an important and energetically demanding calcium turnover throughout their life. The mineralization process occurs by precipitation of calcium carbonate within an organic matrix network of chitin-proteins fibers. Both crystalline and stabilized amorphous polymorphs of calcium carbonate are found in crustacean biominerals. Furthermore, Crustacea is the only phylum of animals able to elaborate and resorb periodically calcified structures. Notably for these two previous reasons, crustaceans are more and more extensively studied and considered as models of choice in the biomineralization research area.

Gene expression profiling of cuticular proteins across the moult cycle of the crab Portunus pelagicus

Background

Crustaceans represent an attractive model to study biomineralization and cuticle matrix formation, as these events are precisely timed to occur at certain stages of the moult cycle. Moulting, the process by which crustaceans shed their exoskeleton, involves the partial breakdown of the old exoskeleton and the synthesis of a new cuticle. This cuticle is subdivided into layers, some of which become calcified while others remain uncalcified. The cuticle matrix consists of many different proteins that confer the physical properties, such as pliability, of the exoskeleton.

Results

We have used a custom cDNA microarray chip, developed for the blue swimmer crab Portunus pelagicus, to generate expression profiles of genes involved in exoskeletal formation across the moult cycle. A total of 21 distinct moult-cycle related differentially expressed transcripts representing crustacean cuticular proteins were isolated. Of these, 13 contained copies of the cuticle_1 domain previously isolated from calcified regions of the crustacean exoskeleton, four transcripts contained a chitin_bind_4 domain (RR consensus sequence) associated with both the calcified and un-calcified cuticle of crustaceans, and four transcripts contained an unannotated domain (PfamB_109992) previously isolated from C. pagurus. Additionally, cryptocyanin, a hemolymph protein involved in cuticle synthesis and structural integrity, also displays differential expression related to the moult cycle. Moult stage-specific expression analysis of these transcripts revealed that differential gene expression occurs both among transcripts containing the same domain and among transcripts containing different domains.

Conclusion

The large variety of genes associated with cuticle formation, and their differential expression across the crustacean moult cycle, point to the complexity of the processes associated with cuticle formation and hardening. This study provides a molecular entry path into the investigation of the gene networks associated with cuticle formation.

Differential expression of eight transcripts and their roles in the cuticle of the blue crab, Callinectes sapidus

Eight cuticle protein transcripts from Callinectes sapidus were sequenced and their expression determined across the molt cycle in both calcifying and arthrodial cuticle hypodermis using quantitative PCR, Northern blots, and in situ hybridization. Four transcripts, designated CsAMP, are found only in non-calcifying arthrodial membrane hypodermis. They all code for a Rebers-Riddiford-1 motif, known to bind chitin. CsAMP9.3 is most likely an exocuticle constituent since it is expressed only during pre-molt. The other three arthrodial transcripts are present both before and after ecdysis. One of these, CsAMP16.3, codes for a RGD cell-attachment motif that could be involved in anchoring chitin-protein fibers to pore canals, cellular extensions of the hypodermis in the cuticle. The other four transcripts, designated CsCP, were found only in calcifying hypodermis. CsCP14.1 contains an RR-1 motif, which is more commonly found in non-calcifying cuticle proteins. CsCP6.1 is expressed post-molt and contains a partial RR motif, suggesting that it could bind to chitin in the endocuticle. The other two transcripts from calcifying hypodermis do not code for RR proteins, but both contain three copies of a different insect cuticle motif. One of these, CsCP19.0, is expressed only post-molt while the other, CsCP15.0, is present both before and after ecdysis.

Preliminary characterisation of repeat families in the genome of EhV-86, a giant algal virus that infects the marine microalga Emiliania huxleyi

EhV-86 is a large double stranded DNA virus with a 407,339 base pair circular genome that infects the globally important microalga Emiliania huxleyi. It belongs to a new genus of viruses termed the Coccolithoviridae within the algal virus family Phycodnaviridae. By plotting the EhV-86 genome against itself in a dot-plot analysis we revealed three families of distinctly different repeat sequences throughout its genome, designated Family A, B and C. Family A repeats are non-coding, found immediately upstream of 86 predicted coding sequences (CDSs) and are likely to play a crucial role in controlling the expression of the associated CDSs. Family B repeats are GC rich, coding and correspond to possible calcium binding sites in 22 proline-rich domains found in the protein products of eight predicted EhV-86 CDSs. Family C repeats are AT-rich, non-coding and are likely to form part of the origin of replication. We suggest that these repeat regions are of fundamental importance during virus propagation being involved with transcriptional control (Family A), virus adsorption/release (Family B) and DNA replication (Family C).

Four differentially expressed cDNAs in Callinectes sapidus containing the Rebers–Riddiford consensus sequence

Decapod crustaceans such as Callinectes sapidus, the blue crab, provide unique opportunities to study proteins involved in biomineralization. Subsequent to each molt, the previously deposited soft cuticle is calcified while the postecdysial layers are simultaneously deposited and mineralized. Though the majority of the exoskeleton hardens, morphologically similar cuticle at the joints, called arthrodial membrane, remains flexible. It seems reasonable that hypodermal cells producing these cuticle types should be synthesizing proteins that regulate mineralization. Data presented here are consistent with this hypothesis, showing that transcripts coding for proteins containing the chitin-binding Rebers-Riddiford (RR) consensus sequence (Gx(8)Gx(7)YxAxExGYx(7)Px(2)P) are differentially expressed. Two RR-containing transcripts, CsAMP8.1 and CsAMP6.0, are found only in arthrodial membrane and are expressed uniformly both before and after ecdysis. They have high sequence homology with RR-containing proteins from uncalcified portions of the cuticle of Cancer pagurus, Penaeus japonicus, and Homarus americanus. The other two transcripts, CsCP8.5 and CsCP8.2, are expressed solely in premolt and in hypodermis depositing calcifying cuticle rather than arthrodial membrane. They have high sequence homology with calcification-associated peptides containing the RR sequence obtained from the calcified cuticle of Procambarus clarkii. This suggests possible involvement in the postmolt mineralization of the pre-ecdysial cuticle.

A crustacean Ca2+-binding protein with a glutamate-rich sequence promotes CaCO3 crystallization

The DD4 mRNA of the penaeid prawn Penaeus japonicus was shown previously to be expressed in the epidermis adjacent to the exoskeleton specifically during the post-moult period, when calcification of the exoskeleton took place. The encoded protein possessed a Ca2+-binding site, suggesting its involvement in the calcification of the exoskeleton. In the present study, an additional ORF (open reading frame) of 289 amino acids was identified at the 5' end of the previous ORF. The newly identified part of the encoded protein included a region of approx. 120 amino acids that was highly rich in glutamate residues, and contained one or more Ca2+-binding sites. In an immunohistochemical study, signals were detected within calcified regions in the endocuticular layer of the exoskeleton. Bacterially expressed partial segments of the protein induced CaCO3 crystallization in vitro. Finally, a reverse transcription-PCR study showed that the expression was limited to an early part of the post-moult period, preceding significant calcification of the exoskeleton. These observations argue for the possibility that the encoded protein, renamed crustocalcin (CCN), promotes formation of CaCO3 crystals in the exoskeleton by inducing nucleation.

Cloning and expression of a cDNA encoding a matrix peptide associated with calcification in the exoskeleton of the crayfish

Calcification-associated peptide (CAP)-1 isolated from the exoskeleton of the crayfish, Procambarus clarkii, has anti-calcification activity and chitin-binding ability and is, therefore, considered to be associated with calcification. In this study, a cDNA encoding CAP-1 was cloned and characterized. An open reading frame encoded a pre-propeptide of 99 amino acid residues, which was composed of a signal peptide, a CAP-1 precursor and two-basic amino acid residues at the C-terminus. The dibasic residues were not observed in the natural CAP-1. Expression analyses using Northern blot and RT-PCR revealed that the mRNA encoding CAP-1 was strongly expressed in the epidermal tissue during the postmolt stage, where and when the calcification takes place. These results support that CAP-1 may play an important role in the calcification of the exoskeleton. Based on the nucleotide sequence of the cDNA encoding CAP-1, a recombinant CAP-1 and that carrying the basic residues at the C-terminus were expressed in Escherichia coli. Anti-calcification assay showed that these recombinant peptides were less active than natural CAP-1, indicating that the phosphate group at the 70th residue, Ser, in natural CAP-1 is important for inhibitory activity and that the paired basic residues have some contribution to the elevation of inhibitory activity.

A novel calcium-binding peptide from the cuticle of the crayfish, Procambarus clarkii

A novel peptide named calcification-associated peptide (CAP)-2 was isolated from the exoskeleton of the crayfish, Procambarus clarkii. CAP-2 consists of 65 amino acid residues and has a 44% sequence identity with CAP-1 characterized previously. It has a chitin-binding domain observed in many arthropod cuticle proteins. CAP-2 showed inhibitory activity on calcium carbonate precipitation and chitin-binding ability. A CAP-2 cDNA was cloned using RT-PCR and RACE and the open reading frame encoded a precursor peptide consisting of a signal peptide and CAP-2. RT-PCR revealed that CAP-2 mRNA was exclusively expressed in the epidermal tissue during the postmolt stage, the site and stage being associated with calcification. Calcium-binding assay using recombinant CAP-2 revealed that this peptide had affinity for calcium ions with a Kd value of about 1 mM. All these results suggest that CAP-2 serves as a nucleator or a regulator in the calcification of the exoskeleton.

Molecular cloning of a cDNA encoding a soluble protein in the coral exoskeleton

Organic substances were extracted from the calcified exoskeleton of the reef coral Galaxea fascicularis. In an SDS-PAGE analysis of the extract, a protein with an apparent molecular mass of 53 kDa was detected as well as two other weaker bands. A Ca2+ overlay analysis failed to find a Ca2+-binding protein in the extract. Periodic acid Schiff staining indicated that the 53 kDa protein was glycosylated. A cDNA containing the entire open reading frame for this protein was obtained. Analysis of the deduced protein sequence suggests that the protein, named galaxin, is synthesized as a precursor consisting of a signal peptide, a propeptide sequence, and a mature protein of 298 amino acids. Galaxin exhibits a novel amino acid sequence which is characterized by a tandem repeat structure. Galaxin transcripts were detected in the adult coral, but not in planktonic larvae.

Characterization and spatiotemporal expression of orchestin, a gene encoding an ecdysone-inducible protein from a crustacean organic matrix

We report the characterization of a new gene encoding an acidic protein named Orchestin. This protein is a component of the organic matrix of calcium storage structures (calcareous concretions) elaborated during the moulting cycles of the terrestrial crustacean Orchestia cavimana. The deduced molecular mass of Orchestin is estimated to be 12.4 kDa and the pI to be 4.4, whereas the native protein extracted from the calcium deposits migrates as a 23 kDa band on SDS/PAGE. This discrepancy is probably due to the richness of this protein in acidic amino acids (approx. 30%). The protein obtained by expressing the Orchestin cDNA in Escherichia coli presents an electrophoretic mobility of 25 kDa. Antibodies raised against the recombinant protein recognize the 23 kDa native protein exclusively among the organic-matrix components. Spatiotemporal analysis of the expression of the orchestin gene shows that it is expressed only in the storage organ cells when the concretions are elaborated during the premoult period and also, to a smaller extent, during the postmoult period. The translation products are expressed in accordance with the transcript expression during both the premoult and postmoult periods. Study of the hormonal stimulation of orchestin reveals that 20-hydroxyecdysone induces this gene as a secondary-response or late-response gene.

The DD5 gene of the decapod crustacean Penaeus japonicus encodes a putative exoskeletal protein with a novel tandem repeat structure

A gene, named DD5, was identified in the penaeid prawn Penaeus japonicus and its cDNA cloned and sequenced. DD5 is expressed in the epidermal cells underlying the exoskeleton and the transcripts are detected specifically during the postmolt stage of the molt cycle. Sequence analysis of the conceptual protein product suggests that the DD5 protein is a component of the exoskeleton. The bulk of the protein consists of tandem repeats of a unit sequence of approximately 100 amino acids. The repeated sequences are highly homologous to one another and each of them includes a variant of the Rebers--Riddiford consensus sequence.