Proteasome properties of hemocytes differ between the whiteleg shrimp Penaeus vannamei and the brown shrimp Crangon crangon (Crustacea, Decapoda)

Characterization of microsatellite markers in the coding regions of the Penaeus vannamei genome

In this study, an extensive analysis of microsatellite markers (Single Tandem Repeats-STRs) in Penaeus vannamei was conducted at an advanced level. The markers were thoroughly examined, characterized, and specific markers located within coding regions were identified. Out of a total of 306 STRs, 117 were classified as perfect markers based on their single repeat motif. Among these perfect markers, 62 were found to be associated with predicted coding genes (mRNA), which were involved in various functions such as binding, catalytic activity, ATP-dependent activity, transcription, structural and molecular regulation. To validate the accuracy of the findings, a sample of nine markers was subjected to in vitro testing, which confirmed the presence of polymorphisms within the population. These results suggest the existence of different protein isoforms within the population, indicating the potential of these markers for application in both population and phenotype-genotype association studies. This innovative approach opens up new possibilities for investigating the impact of genomic plasticity in populations of P. vannamei.

Proteomics of the haemolymph of the terrestrial crustacean Porcellio scaber reveals components of its innate immunity under baseline conditions

The terrestrial crustacean Porcellio scaber is an established test organism in environmental research. We analysed the haemolymph proteome of P. scaber using a classical proteomic approach based on one-dimensional gel electrophoresis and tandem mass spectrometry. Using a publicly available protein database and our P. scaber transcriptome data, we have identified 76 proteins involved in cytoskeleton formation, protein degradation, vesicular transport, genetic information processing, detoxification, carbohydrate and lipid metabolism reflecting haemocyte metabolic activity, active intracellular transport, and intercellular communication. Compared with the data reported for other crustaceans, 28 of these P. scaber proteins have been linked to its immunity, among them hemocyanin, α-2-macroglobulin, phenoloxidase 3, superoxide dismutase, glutathione S-transferase, haemolymph clottable protein, and histones H4 and H2B. Our results thus provide a firm base for studying the innate immune response of P. scaber at the level of the haemolymph proteome. This knowledge is of particular importance in ecotoxicity studies with various environmental stressors where understanding physiological changes is important to reveal possible modes of action.

Orally administered nano-polystyrene caused vitellogenin alteration and oxidative stress in the red swamp crayfish (Procambarus clarkii)

Nanoplastics (≤100 nm) represent the smallest fraction of plastic litter and may result in the aquatic environment as degradation products of larger plastic material. To date, few studies focused on the interactions of micro- and nanoplastics with freshwater Decapoda. The red swamp crayfish (Procambarus clarkii, Girard, 1852) is an invasive species able to tolerate highly perturbed environments. As a benthic opportunistic feeder, this species may be susceptible to plastic ingestion. In this study, adult P. clarkii, at intermolt stage, were exposed to 100 μg of 100 nm carboxylated polystyrene nanoparticles (PS NPs) through diet in a 72 h acute toxicity test. An integrated approach was conceived to assess the biological effects of PS NPs, by analyzing both transcriptomic and physiological responses. Total hemocyte counts, basal and total phenoloxidase activities, glycemia and total protein concentration were investigated in crayfish hemolymph at 0 h, 24 h, 48 h and 72 h from PS NPs administration to evaluate general stress response over time. Differentially expressed genes (DEGs) in the hemocytes and hepatopancreas were analyzed to ascertain the response of crayfish to PS NP challenge after 72 h. At a physiological level, crayfish were able to compensate for the induced stress, not exceeding generic stress thresholds. The RNA-Sequencing analysis revealed the altered expression of few genes involved in immune response, oxidative stress, gene transcription and translation, protein degradation, lipid metabolism, oxygen demand, and reproduction after PS NPs exposure. This study suggests that a low concentration of PS NPs may induce mild stress in crayfish, and sheds light on molecular pathways possibly involved in nanoplastic toxicity.

Extracellular Vesicles and Post-Translational Protein Deimination Signatures in Mollusca-The Blue Mussel (Mytilus edulis), Soft Shell Clam (Mya arenaria), Eastern Oyster (Crassostrea virginica) and Atlantic Jacknife Clam (Ensis leei)

Simple Summary

Oysters and clams form an important component of the food chain and food security and are of considerable commercial value worldwide. They are affected by pollution and climate change, as well as a range of infections, some of which are opportunistic. For aquaculture purposes they are furthermore of great commercial value and changes in their immune responses can also serve as indicators of changes in ocean environments. Therefore, studies into understanding new factors in their immune systems may aid new biomarker discovery and are of considerable value. This study assessed new biomarkers relating to changes in protein function in four economically important marine molluscs, the blue mussel, soft shell clam, Eastern oyster, and Atlantic jacknife clam. These findings indicate novel regulatory mechanisms of important metabolic and immunology related pathways in these mollusks. The findings provide new understanding to how these pathways function in diverse ways in different animal species as well as aiding new biomarker discovery for Mollusca aquaculture.

Abstract

Oysters and clams are important for food security and of commercial value worldwide. They are affected by anthropogenic changes and opportunistic pathogens and can be indicators of changes in ocean environments. Therefore, studies into biomarker discovery are of considerable value. This study aimed at assessing extracellular vesicle (EV) signatures and post-translational protein deimination profiles of hemolymph from four commercially valuable Mollusca species, the blue mussel (Mytilus edulis), soft shell clam (Mya arenaria), Eastern oyster (Crassostrea virginica), and Atlantic jacknife clam (Ensis leei). EVs form part of cellular communication by transporting protein and genetic cargo and play roles in immunity and host–pathogen interactions. Protein deimination is a post-translational modification caused by peptidylarginine deiminases (PADs), and can facilitate protein moonlighting in health and disease. The current study identified hemolymph-EV profiles in the four Mollusca species, revealing some species differences. Deiminated protein candidates differed in hemolymph between the species, with some common targets between all four species (e.g., histone H3 and H4, actin, and GAPDH), while other hits were species-specific; in blue mussel these included heavy metal binding protein, heat shock proteins 60 and 90, 2-phospho-D-glycerate hydrolyase, GTP cyclohydrolase feedback regulatory protein, sodium/potassium-transporting ATPase, and fibrinogen domain containing protein. In soft shell clam specific deimination hits included dynein, MCM3-associated protein, and SCRN. In Eastern oyster specific deimination hits included muscle LIM protein, beta-1,3-glucan-binding protein, myosin heavy chain, thaumatin-like protein, vWFA domain-containing protein, BTB domain-containing protein, amylase, and beta-catenin. Deiminated proteins specific to Atlantic jackknife clam included nacre c1q domain-containing protein and PDZ domain-containing protein In addition, some proteins were common as deiminated targets between two or three of the Bivalvia species under study (e.g., EP protein, C1q domain containing protein, histone H2B, tubulin, elongation factor 1-alpha, dominin, extracellular superoxide dismutase). Protein interaction network analysis for the deiminated protein hits revealed major pathways relevant for immunity and metabolism, providing novel insights into post-translational regulation via deimination. The study contributes to EV characterization in diverse taxa and understanding of roles for PAD-mediated regulation of immune and metabolic pathways throughout phylogeny.

Extracellular vesicles and post-translational protein deimination signatures in haemolymph of the American lobster (Homarus americanus)

The American lobster (Homarus americanus) is a commercially important crustacean with an unusual long life span up to 100 years and a comparative animal model of longevity. Therefore, research into its immune system and physiology is of considerable importance both for industry and comparative immunology studies. Peptidylarginine deiminases (PADs) are a phylogenetically conserved enzyme family that catalyses post-translational protein deimination via the conversion of arginine to citrulline. This can lead to structural and functional protein changes, sometimes contributing to protein moonlighting, in health and disease. PADs also regulate the cellular release of extracellular vesicles (EVs), which is an important part of cellular communication, both in normal physiology and in immune responses. Hitherto, studies on EVs in Crustacea are limited and neither PADs nor associated protein deimination have been studied in a Crustacean species. The current study assessed EV and deimination signatures in haemolymph of the American lobster. Lobster EVs were found to be a poly-dispersed population in the 10-500 nm size range, with the majority of smaller EVs, which fell within 22-115 nm. In lobster haemolymph, 9 key immune and metabolic proteins were identified to be post-translationally deiminated, while further 41 deiminated protein hits were identified when searching against a Crustacean database. KEGG (Kyoto encyclopedia of genes and genomes) and GO (gene ontology) enrichment analysis of these deiminated proteins revealed KEGG and GO pathways relating to a number of immune, including anti-pathogenic (viral, bacterial, fungal) and host-pathogen interactions, as well as metabolic pathways, regulation of vesicle and exosome release, mitochondrial function, ATP generation, gene regulation, telomerase homeostasis and developmental processes. The characterisation of EVs, and post-translational deimination signatures, reported in lobster in the current study, and the first time in Crustacea, provides insights into protein moonlighting functions of both species-specific and phylogenetically conserved proteins and EV-mediated communication in this long-lived crustacean. The current study furthermore lays foundation for novel biomarker discovery for lobster aquaculture.

Transcriptional Identification of Related Proteins in the Immune System of the Crayfish Procambarus clarkii

The freshwater crayfish Procambarus clarkii is an animal model employed for physiological and immunological studies and is also of great economic importance in aquaculture. Although it is a species of easy husbandry, a high percentage of its production is lost annually as a result of infectious diseases. Currently, genetic information about the immune system of crustaceans is limited. Therefore, we used the abdominal nerve cord from P. clarkii to obtain its transcriptome using Next Generation Sequencing (NGS) to identify proteins that participate in the immune system. The reads were assembled de novo and consensus sequences with more than 3000 nucleotides were selected for analysis. The transcripts of the sequences of RNA were edited for annotation and sent to the GenBank database of the National Center for Biotechnology Information (NCBI). We made a list of accession numbers of the sequences which were organized by the putative role of the immune system pathway in which they participate. In this work, we report on 80 proteins identified from the transcriptome of crayfish related to the immune system, 74 of them being the first reported for P. clarkii. We hope that the knowledge of these sequences will contribute significantly to the development of future studies of the immune system in crustaceans.