Marine Biotechnology最新文献

Mollusk shell formation is a delicate and comprehensive physiological process that relies on the precise deposition of crystals under the control of shell matrix proteins. However, the underlying protective mechanisms governing this process remain largely unknown. Herein, a novel shell matrix protein gene was identified from the freshwater mussel, Hyriopsis cumingii. The predicted protein is characterized by a high glycine content and two Kunitz-type SPI domains, designated as HcGrKuSPI. The HcGrKuSPI gene was highly expressed in the outer epithelial of the mantle edge and mantle pallial. Immunostaining in situ analysis revealed the presence of HcGrKuSPI in the thick inter-prism matrix of the prismatic layer and the organic membrane of the nacreous layer. The expression of HcGrKuSPI in the pearl sac significantly increased during the ordered deposition of pearl nacre tablets. The resultant recombinant protein, SUMO-HcGrKuSPI, exhibited a strong affinity for aragonite and calcite and was involved in the morphological modification of calcite crystals in vitro. These results indicate that HcGrKuSPI is involved in organic framework construction and crystal morphological modification during the prismatic and nacreous layers formation. Furthermore, the expression of HcGrKuSPI in the mantle significantly increased following bacterial infection within the extrapallial fluid, and SUMO-HcGrKuSPI exhibited a strong inhibitory effect against bacterial growth and trypsin activity. Antibody injection in vivo led to severe damage to the thick inter-column framework of the prismatic layer and morphological deformities of nacre tablets. These findings indicate that HcGrKuSPI exhibits excellent protease inhibitory and antibacterial activities, providing a matrix protection system to ensure the smoothness of shell and pearl formation. Overall, these results enhance our understanding of the protective mechanisms involved in mollusk biomineralization.

Genome research has dominated life sciences research in the last two decades. Of approximately 11,000 sequenced vertebrate genomes, genomes of teleost fish represent about 30%, with reference genome sequences available for most aquaculture fish species. While such progress has accelerated progress in aquaculture genetics research and breeding, it is clear that understanding of full genomic variations among aquaculture species is lacking. This is largely because of the way reference genomic sequences were produced, with a single or just a few genomes being sequenced. In addition, haplotype variations and their representation in the species or population are unknown. This hinders understanding of genomic basis of phenotypic variations relevant to performance and production traits such as growth rates, feed conversion efficiency, disease resistance, stress responses, processing yields, and reproductive traits, among other traits, especially so with strain-specific performance traits. The pangenome refers to a whole collection of genomic sequences found in the entire species or population rather than in a single individual, as represented in reference genomes. Pangenome includes the core genome sequence that are shared in all individuals, and variable or dispensable genome sequence found in a subset of individuals, representing intraspecies genomic variations. In this review, we present the current state of reference genomes and reference pangenomes, compare the advantages and disadvantages of various methods in producing pangenomes, propose the concept of pangenome plus (pangenome⁺) to include genomes of related species with which interspecific hybrids can be made to introgress the beneficial genes. Revealing full genomic variations, determination of genomic variations relevant to performance traits, and combining beneficial genes and alleles into aquaculture breeds are three most important steps for the application of genome-based technologies to aquaculture breeding. To accomplish these three steps is challenging but offers unprecedented opportunities for aquaculture.

Developing effective molecular indicators to monitor stress status of coastal species is a top priority due to the impacts of climate change. However, the complexity of stress responses, which are regulated by multiple genes, limits the effectiveness of single-gene approaches in accurately reflecting stress status. Transcription factors (TFs) are promising candidates for comprehensively assessing stress responses, as they regulate numerous stress-responsive genes. In this study, we present a framework for identifying TF indicators that reflect the stress status of Pacific oysters (Crassostrea gigas). Specifically, oysters were exposed to high, medium, and low tide conditions to assess the physiological responses of oysters to tidal-induced stress. Enrichment analysis of differentially accessible chromatin peaks derived from assay for transposase-accessible chromatin sequencing (ATAC-seq) identified several key TFs. Among these, CCCTC-binding factor (Cg-CTCF) and MYB proto-oncogene A (Cg-MYBA) were significantly upregulated under tidal-induced stress and occupied critical positions in regulatory networks, as indicated by RNA-seq. RNA interference experiments confirmed that both genes contribute to enhancing survival under heat stress, a major stressor affecting oysters. Additionally, field experiments demonstrated significant upregulation of these genes under natural stress conditions, suggesting their potential as indicators for oyster reef management. To our knowledge, this is the first study on the coastal invertebrate to combine ATAC/RNA-seq with in vivo TF knockdown and field validation to propose TFs as practical stress indicators. We advocate for the broad application of our framework to explore TFs as molecular indicators of health status in marine organisms, thereby enabling informed strategies for conservation management.

In DUI animals, two sex-specific mitochondrial lineages are present: one transmitted maternally (F-type) and the other paternally (M-type), each containing a sex-specific mitochondrial ORFan gene. Comprehensive in silico characterization of DUI ORFan proteins has been conducted in freshwater mussels, with partial studies in marine mussels; however, research in other DUI species remains scarce. In this regard, we newly identified two DUI species, Antigona lamellaris (Schumacher, 1817) and Ezocallista brevisiphonata (P. P. Carpenter, 1864), and analyzed the major unassigned regions of the mitochondrial genomes in 169 specimens from eight species of Veneridae, verifying the presence of novel mitochondrial ORFs. Structural and functional analyses were performed on 14 ORFans, and the conservation patterns and properties of DUI ORFans in Veneridae were further explored by integrating in silico characterization results from freshwater and marine mussels. Strong structural and functional similarities were found between F-ORF and M-ORF proteins, both across different bivalve species and within the studied species. In contrast to freshwater and marine mussels, the F and M-ORF sequences in Veneridae show remarkable similarity. Additionally, apart from sex-specific ORFs, reverse ORFs (ORFs encoded on the reverse strand) were identified in Antigona lamellaris. Predicted transmembrane (TMs) number and topology analysis suggest that ORFs in Veneridae exhibit lower conservation compared to those in freshwater mussels. Our findings support the hypothesis that ORFans may originate from viruses or from proteins involved in mitochondrial energy production, providing further evidence for the multiple origins of ORFs. We propose that Veneridae, freshwater mussels, and marine mussels may harbor DUI systems with distinct origins and modes of action. The connection between ORFan proteins and DUI systems may differ across these taxa.

At present, shells have been used to incubate Pyropia haitanensis (P. haitanensis) shell-boring conchocelis. To develop a more convenient substrate for P. haitanensis conchocelis cultivation, a novel P. haitanensis shell-boring conchocelis culture substrate (CaCO₃/LPE/CA) was developed from calcite, low-density polyethylene, and calcium alginate. The mechanical properties and stability of CaCO₃/LPE/CA, including implanting density (ID) and Yield per unit area, were tested. The results showed that the CaCO₃/LPE/CA met practical P. haitanensis shell-boring conchocelis breeding application requirements. P. haitanensis was successfully cultured on CaCO₃/LPE/CA, and its life cycle was observed through biomicroscopy and scanning electron microscopy (SEM). After conchospores was succrssfully reseased from P. haitanensis conchosporangial branch, the movement and germination of conchospores were also observed. The yield of conchospores per unit area of optimized CaCO₃/LPE/CA reached 369.6 × 10³ conchospores/cm², making it a suitable candidate for P. haitanensis shell-boring conchocelis cultivation. Overall, CaCO₃/LPE/CA exhibits great potential as a marine bioactive material, and the process and cost of P. haitanensis culture breeding could be simplified due to its comprehensive characteristics.

Litopenaeus vannamei is one of the most widely farmed shrimp species worldwide, but it traditionally exhibits limited adaptability to low-salinity environments. Genetic improvement through intraspecific hybridization has been proven effective in enhancing environmental adaptability. This study aimed to elucidate the molecular mechanisms underlying the low-salinity adaptation of a hybrid shrimp strain selected through intraspecific hybridization. Shrimp were reared for 12 weeks under salinity conditions of 1 practical salinity unit (PSU) and 15 practical salinity units (PSU). By conducting a combined analysis of transcriptomics and metabolomics, we explored the low-salt adaptation mechanism of the hybrid shrimp. We found that they enhanced their adaptability through self-osmotic regulation and energy regulation. Transcriptome results revealed that genes associated with calcium-activated chloride channels, chloride transporters, and sodium-driven chloride/bicarbonate exchangers were up-regulated, suggesting enhanced ion transport capacity under low salinity. The metabolomics results indicated that key enzymes involved in glycolysis and gluconeogenesis, including phosphofructokinase and phosphoenolpyruvate carboxykinase, showed increased abundance, indicating elevated energy metabolism to support osmotic adjustment. Overall, the selected hybrid shrimp enhanced osmotic regulation by strengthening energy metabolism to improve their low-salt adaptability. These findings provide valuable insights for future genetic breeding and sustainable shrimp aquaculture in low-salinity regions.

Antimicrobial resistance is a serious threat to global public health and requires new therapeutic approaches. Antimicrobial peptides (AMP) are recognized as promising candidates to address antimicrobial resistance. AMP can disrupt cell membranes by increasing permeability and causing lysis, or they can also interact with intracellular targets to inhibit essential metabolic processes. The genus Acropora is regarded as a valuable source for bioprospecting antimicrobial compounds. In this study, we employed in silico analytical strategies to predict potential antibacterial activity using AMPs derived from transcriptomes of multiple life cycle stages of the coral Acropora digitifera, as well as from cultured cells originating from adult coral tissues. The analysis involved multiple sequence alignments, Hidden Markov models, machine learning algorithms, structural modeling, physicochemical property assessment, and molecular docking. From the transcriptomic data, 15 sequences with potential antimicrobial activity were identified. Five AMPs were further evaluated for their binding efficacy against the TolC and OprM protein channels of RND-type transporter proteins, as well as DNA gyrase B of Klebsiella pneumoniae, Pseudomonas aeruginosa, and Escherichia coli. Binding free energy analysis indicated that AMP-Ad2 exhibited the most favorable interaction with the TolC channel of E. coli. AMP-Ad3 showed the highest binding affinity with the OprM channel of P. aeruginosa, while AMP-Ad15 displayed the most favorable binding energy for the TolC channel of K. pneumoniae. The strongest interaction overall was observed between AMP-Ad15 and the DNA gyrase B of K. pneumoniae. These results demonstrate the utility of in silico prediction tools for identifying AMP candidates from A. digitifera transcriptomes and provide a basis for the planned synthesis and in vitro evaluation of these peptides, aiming to assess their therapeutic potential against resistant Gram-negative bacteria.

Fish skeletal muscle serves as a crucial source of high-quality protein for human consumption. MicroRNAs (miRNAs) are important epigenetic regulators for the growth and development of skeletal muscle. Although the functions of many myogenic miRNAs have been studied, the regulatory functions of miRNAs in fish skeletal muscle have not been fully investigated. Here we show miR-125b is highly expressed in fast muscle of Chinese perch (Siniperca chuatsi) at 30–60 days post-hatching (dph), with transient downregulation during the skeletal muscle injury repair stage, implying its essential regulatory role in fast muscle growth and injury repair. Moreover, inhibiting miR-125b in Chinese perch resulted in an increase in muscle fiber diameter, the number of proliferating myoblasts and nuclei in single muscle fiber. In contrast, overexpression of miR-125b in Chinese perch led to a significant reduction in muscle fiber diameter, accompanied by a significant decrease in the number of proliferating myoblasts and the number of nuclei in single muscle fiber. Bioinformatics analysis and dual luciferase assays confirmed MyoD and Myomaker as direct targets of miR-125b. In summary, our findings demonstrate that miR-125b modulates the expression of MyoD and Myomaker, thereby regulating the proliferation and fusion of myoblasts, and ultimately controlling the hypertrophy of muscle fibers in Chinese perch. This finding holds significant relevance in unraveling the genetic mechanisms that govern the developmental traits of muscle fibers in fish during the postembryonic phase.

The unreported peptide versicotide K (1), along with known averufin (2), 1′- hydroxyversicolorin B (3), averufanin (4), and sterigmatocystin (5), was isolated from the sponge-derived fungal strain Aspergillus versicolor 01NT- 1.5.1. Moreover, the new 6,8-dimethoxyaverythrin (6) and known averythrin (7) and sclerotiotide F (8) were isolated from another sponge-derived fungus Aspergillus flavus КMM 4695 (= VO49-48.3). The antimicrobial and cytotoxic activities of the isolated compounds were studied. The obtained data on the low cytotoxicity of averufanin (4) to normal HaCaT keratinocytes and H9c2 cardiomyocytes confirms its anticancer potential for future research. The significant activity of averythrin (7) against Staphylococcus aureus growth and biofilm formation (IC₅₀ of approximately 10 µM) is the first. The anti-inflammatory activity of versicotide K (1) was predicted using the PASS online server. Moreover, SwissTargetPrediction services predicted COX2 as a possible target for 1, and the interaction of 1 with COX2 was calculated using a molecular docking approach. In in vitro experiments, versicotide K (1) reduced S. aureus infection and ischemia/reperfusion damage of H9c2 cells and prevented TNF-α induced damage of H9c2 cardiomyocytes by 24%, confirming its anti-inflammatory properties.