High-throughput identification of heavy metal binding proteins from the byssus of chinese green mussel (Perna viridis) by combination of transcriptome and proteome sequencing

Integrated transcriptomic and metabolomic approaches reveal molecular response and potential biomarkers of the deep-sea mussel Gigantidas platifrons to copper exposure

Metal pollution caused by deep-sea mining activities has potential detrimental effects on deep-sea ecosystems. However, our knowledge of how deep-sea organisms respond to this pollution is limited, given the challenges of remoteness and technology. To address this, we conducted a toxicity experiment by using deep-sea mussel Gigantidas platifrons as model animals and exposing them to different copper (Cu) concentrations (50 and 500 μg/L) for 7 days. Transcriptomics and LC-MS-based metabolomics methods were employed to characterize the profiles of transcription and metabolism in deep-sea mussels exposed to Cu. Transcriptomic results suggested that Cu toxicity significantly affected the immune response, apoptosis, and signaling processes in G. platifrons. Metabolomic results demonstrated that Cu exposure disrupted its carbohydrate metabolism, anaerobic metabolism and amino acid metabolism. By integrating both sets of results, transcriptomic and metabolomic, we find that Cu exposure significantly disrupts the metabolic pathway of protein digestion and absorption in G. platifrons. Furthermore, several key genes (e.g., heat shock protein 70 and baculoviral IAP repeat-containing protein 2/3) and metabolites (e.g., alanine and succinate) were identified as potential molecular biomarkers for deep-sea mussel's responses to Cu toxicity. This study contributes novel insight for assessing the potential effects of deep-sea mining activities on deep-sea organisms.

Efficient secretion of mussel adhesion proteins using a chaperone protein Spy as fusion tag in Bacillus subtilis

BACKGROUND

Mussel foot proteins (Mfps) are considered as remarkable materials due to their extraordinary adhesive capability. Recombinant expression is an ideal way to synthesis these proteins at large scale. However, secretory expression of Mfps into culture medium has not been achieved in a heterologous host.

METHODS AND RESULTS

Here, to realize the secretion of Mfp3 and Mfp5 in Bacillus subtilis, signal peptide screening was first performed. Minimal Mfp3-6×His was targeted into the growth medium with AmyE signal peptide. We found that a small chaperone protein Spy was secreted efficiently in B. subtilis, and the fusion proteins Spy-Mfp3-6×His and Spy-Mfp5-6×His could also be delivered into growth medium well. The yield of Spy-Mfp3-6×His and Spy-Mfp5-6×His reached 255 and 119 mg L-1 at shake flask conditions, respectively. Mfp3-6×His and Mfp5-6×His were finally purified via TEV protease cleavage and NTA affinity chromatography.

CONCLUSION

Mfp3-6×His and Mfp5-6×His could be efficiently secreted using a chaperone protein Spy as fusion tag in B. subtilis.

The lysosome-phagosome pathway mediates immune regulatory mechanisms in Mesocentrotus nudus against Vibrio coralliilyticus infection

Sea urchins are a popular model species for studying invertebrate diseases. The immune regulatory mechanisms of the sea urchin Mesocentrotus nudus during pathogenic infection are currently unknown. This study aimed to reveal the potential molecular mechanisms of M. nudus during resistance to Vibrio coralliilyticus infection by integrative transcriptomic and proteomic analyses. Here, we identified a total of 135,868 unigenes and 4,351 proteins in the four infection periods of 0 h, 20 h, 60 h and 100 h in M. nudus. In the I20, I60 and I100 infection comparison groups, 10,861, 15,201 and 8,809 differentially expressed genes (DEGs) and 2,188, 2,386 and 2,516 differentially expressed proteins (DEPs) were identified, respectively. We performed an integrated comparative analysis of the transcriptome and proteome throughout the infection phase and found very a low correlation between transcriptome and proteome changes. KEGG pathway analysis revealed that most upregulated DEGs and DEPs were involved in immune strategies. Notably, "lysosome" and "phagosome" activated throughout the infection process, could be considered the two most important enrichment pathways at the mRNA and protein levels. The significant increase in phagocytosis of infected M. nudus coelomocytes further demonstrated that the lysosome-phagosome pathway played an important immunological role in M. nudus resistance to pathogenic infection. Key gene expression profiles and protein‒protein interaction analysis revealed that cathepsin family and V-ATPase family genes might be key bridges in the lysosome-phagosome pathway. In addition, the expression patterns of key immune genes were verified using qRT‒PCR, and the different expression trends of candidate genes reflected, to some extent, the regulatory mechanism of immune homeostasis mediated by the lysosome-phagosome pathway in M. nudus against pathogenic infection. This work will provide new insights into the immune regulatory mechanisms of sea urchins under pathogenic stress and help identify key potential genes/proteins for sea urchin immune responses.

In the footsteps of sea stars: deciphering the catalogue of proteins involved in underwater temporary adhesion

Sea stars adhere strongly but temporarily to underwater substrata via the secretion of a blend of proteins, forming an adhesive footprint that they leave on the surface after detachment. Their tube feet enclose a duo-gland adhesive system comprising two types of adhesive cells, contributing different layers of the footprint and de-adhesive cells. In this study, we characterized the catalogue of sea star footprint proteins (Sfps) in the species Asterias rubens to gain insights in their potential function. We identified 16 Sfps and mapped their expression to type 1 and/or type 2 adhesive cells or to de-adhesive cells by double fluorescent in situ hybridization. Based on their cellular expression pattern and their conserved functional domains, we propose that the identified Sfps serve different functions during attachment, with two Sfps coupling to the surface, six providing cohesive strength and the rest forming a binding matrix. Immunolabelling of footprints with antibodies directed against one protein of each category confirmed these roles. A de-adhesive gland cell-specific astacin-like proteinase presumably weakens the bond between the adhesive material and the tube foot surface during detachment. Overall, we provide a model for temporary adhesion in sea stars, including a comprehensive list of the proteins involved.

Comparative proteomics for an in-depth understanding of bioadhesion mechanisms and evolution across metazoans

Bioadhesion is a critical process for many marine and freshwater invertebrate animals. Bioadhesives mainly made of proteins have remarkable adhesive ability underwater. Unraveling the molecular composition of bioadhesives is fundamental to understanding their physiological roles as well as their potential for biotechnology applications and antibiofouling strategies. With the development of high-throughput methods such as proteomics, bioadhesive protein data in diverse taxa are rapidly accumulating, but the common mechanism across species is elusive due to the vast variety of bioadhesives. In this review, bioadhesive proteins from various taxa are reviewed, with the aim of facilitating researchers to appreciate the diversity of bioadhesive proteins (mostly 20-40) across species. By comparing proteomes across species, it was found that glycine-rich, epidermal growth factor, peroxidase, and DOPA together with typical extracellular domains are the most commonly used domains. Additionally, permanent and temporary adhesion show obvious differences in terms of domains or proteins. A basic recipe for bioadhesives composed of six components is proposed: structural elements, extracellular domains, modification enzymes, proteinase inhibitors, cytoskeletal proteins, and others. The extracellular domains are mostly related to interactions with other macromolecules (proteins, carbohydrates, and lipids), suggesting that domain shuffling and macromolecule interaction might be fundamental for bioadhesive evolution.

Genomics and Transcriptomics of the green mussel explain the durability of its byssus

Mussels, which occupy important positions in marine ecosystems, attach tightly to underwater substrates using a proteinaceous holdfast known as the byssus, which is tough, durable, and resistant to enzymatic degradation. Although various byssal proteins have been identified, the mechanisms by which it achieves such durability are unknown. Here we report comprehensive identification of genes involved in byssus formation through whole-genome and foot-specific transcriptomic analyses of the green mussel, Perna viridis. Interestingly, proteins encoded by highly expressed genes include proteinase inhibitors and defense proteins, including lysozyme and lectins, in addition to structural proteins and protein modification enzymes that probably catalyze polymerization and insolubilization. This assemblage of structural and protective molecules constitutes a multi-pronged strategy to render the byssus highly resistant to environmental insults.