Prawn lipocalin: characterization of a color shift induced by gene knockdown and ligand binding assay

Study on the Regulatory Mechanisms of Carapace Marking Formation in Marsupenaeus japonicus

There are two phenotypes in the natural populations of Marsupenaeus japonicus, which is an ideal model for studying the formation of markings and body color in crustaceans. In a previous study, we used comparative transcriptome technology to screen some functional genes related to body color regulation. Here, high-throughput sequencing technology was used to perform microRNA (miRNA) sequencing analysis on the exoskeleton of M. japonicus with two types of carapace markings, and functional studies of related genes were performed. A total of 687 mature miRNAs belonging to 135 miRNA families were identified in this study, and 111 novel miRNAs were found. Through stringent screening conditions, a total of 18 differentially expressed miRNAs were identified, including 14 with upregulated expression and 4 with downregulated expression. Multiple target genes were predicted for almost all of the differentially expressed miRNAs. The expression levels of several target genes, such as those related to cytoplasmic microtubule organization, transmembrane transportation, and signal transduction, were confirmed using qRT-PCR. This study revealed that both the CRCN A2 and CRCN C1 genes were highly expressed in type I individuals, while the expression levels of their related miRNAs in type I individuals were lower than those in type II individuals, which is consistent with the mechanism of miRNAs negatively regulating mRNA expression. Through interference with the CRCN A2 and CRCN C1 genes, a clear regulatory relationship was found between the two genes, and the dendritic xanthophores in the carapace of M. japonicus gradually changed from bright yellow to dark black, with obvious shrinkage. In summary, our studies provide references for the regulatory mechanisms of marking formation in M. japonicus.

Enhancing the color and stress tolerance of cherry shrimp (Neocaridina davidi var. red) using astaxanthin and Bidens Pilosa

This study aimed to evaluate the effects of different concentrations of astaxanthin and Bidens Pilosa compound feed additives on the color and hypoxia tolerance of cherry shrimp (Neocaridina davidi var. red). Color parameters were assessed using CIELAB color space, and differential gene expression related to color and stress was analyzed using reverse transcription quantitative polymerase chain reaction (RT-qPCR) to understand the gene regulatory mechanisms affecting color expression and stability. Over a 56-day rearing period, the feed additives AX100 (astaxanthin 100 mg/kg) and AX100+BP (astaxanthin 100 mg/kg + B. pilosa 5 g/kg) significantly reduced the color difference values compared to the standard sample (ΔE*ab), indicating notable color boosting effects. This included a reduction in lightness (L*), a decrease in color hue angle (h*) with AX100, and an increase in redness (a*) and chroma (C*) with AX100+BP. We further designed 22 color-related gene primers, 16 of which amplified the target fragment. Six gene sets exhibited significant differences among all feed treatment groups and were correlated with color expression. After 9 hours of hypoxic stress, body color remained stable in the feed additive groups, especially in the AX100 + BP and AX200 + BP (astaxanthin 200 mg/kg + B. pilosa 5 g/kg) groups, with color differences before and after hypoxic stress remaining below the discernible threshold of the human eye, indicating optimal color stability. Additionally, the CAT gene, among the stress-related genes that successfully amplified, showed significant differences among feed treatment groups and correlated with color stability based on color difference values. In conclusion, the composite addition of 100 mg/kg astaxanthin and 5 g/kg Bidens pilosa (AX100 + BP) was identified as the most effective treatment. This formulation significantly enhanced cherry shrimp color, evidenced by improved parameters such as decreased lightness and increased redness. Moreover, AX100 + BP demonstrated superior color stability under hypoxic conditions, with ΔE*ab values remaining below the discernible threshold of the human eye, highlighting its potential for maintaining optimal color during transportation. Offering a basis for enhancing the commercial value and reducing the sale risks of cherry shrimp.

Genome-wide identification of crustacyanin and function analysis of one isoform high-expression in carapace from Neocaridina denticulata sinensis

Lipocalin proteins transport hydrophobic molecules, including apolipoprotein D, retinol-binding protein, and crustacyanin (CRCN). CRCN can combine with astaxanthin to cause a bathochromic shift in the emission spectrum of astaxanthin from red to blue. Therefore, CRCN influences the colors and patterns of crustaceans, which are important for various biological functions such as camouflage, reproduction, and communication. For aquatic organisms, body color is economically important and can be indicative of habitat water quality. In this study, thirteen CRCN genes (NdCRCNs) were first discovered in Neocaridina denticulata sinensis, contradicting prior findings of a few isoform genes in a species. The expression pattern of NdCRCNs in tissues showed that the expression of one CRCN isoform gene, named NdCRCN-30, was the highest in the carapace. In situ hybridization (ISH) analysis revealed that NdCRCN-30 was predominantly distributed in the outer epidermis of shrimp. Interference of NdCRCN-30 could cause a change in the color of the carapace. RNA-seq was performed after knockdown with the NdCRCN-30, and differential gene enrichment analysis revealed that this gene is primarily associated with antioxidant function, pigmentation, and molting. Overall, our results will provide new insights into the biological function of the CRCN and genetic breeding for changing body color in economic crustaceans.

Insights into the mechanism of color formation of the freshwater prawn (Macrobrachium rosenbergii) revealed by de novo assembly transcriptome analysis

Body color is an important visual indicator of crustacean quality and plays a major role in consumer acceptability, perceived quality, and the market price of crustaceans. The freshwater prawn (Macrobrachium rosenbergii) has two distinct phenotypic variations, characterized by dark blue and light yellow body colors. However, the underlying mechanisms regulating the body color of M. rosenbergii remain unclear. In this study, the composition of shell color parameters and pigment cells of raw and cooked dark blue and light yellow M. rosenbergii was investigated and the mechanisms associated with body color were elucidated by transcriptome analysis. The results showed significant differences in the raw shells of the dark blue and light yellow M. rosenbergii (L: 26.20 ± 0.53 vs. 29.25 ± 0.45; a: -0.88 ± 0.19 vs. 0.35 ± 0.18; b: 1.73 ± 0.20 vs. 3.46 ± 0.37; dE: 70.33 ± 0.53 vs. 67.34 ± 0.45, respectively, p = 0.000) as well as the cooked shells (L: 58.14 ± 0.81 vs. 55.78 ± 0.55; a: 19.30 ± 0.56 vs. 16.42 ± 0.40; b: 23.60 ± 0.66 vs. 20.30 ± 0.40, respectively, p < 0.05). Transcriptome differential gene analysis obtained 39.02 Gb of raw data and 158,026 unigenes. Comprehensive searches of the SwissProt, Nr, KEGG, Pfam, and KOG databases resulted in successful annotations of 23,902 (33 %), 40,436 (25.59 %), 32,015 (20.26 %), 26,139 (16.54 %), and 22,155 (14.02 %) proteins, respectively. By KEGG pathway analysis, numerous differentially expressed genes were related to pigmentation-related pathways (MAPK signaling pathway, Wnt signaling pathway, melanin production, tyrosine metabolism, and cell-cell communication process). Candidate DEGs that may be involved in body color included apolipoprotein D, crustacyanin, cytochrome P450, and tyrosinase, as verified by quantitative real-time PCR. The results of this study provide useful references to further elucidate the molecular mechanisms of color formation of M. rosenbergii and other crustaceans.

The comparison of morphology and transcriptome in the inner membrane reveals the potential mechanism of the heritable carapace color of the Chinese mitten crab Eriocheir sinensis

Carapace color plays an important role in the communication, reproduction, and self-defense of crustaceans, which is also related to their economic value. Chinese mitten crab (Eriocheir sinensis) is an important aquaculture species in China, and there are different strains with heritable carapace colors, i.e. Green, White, and Red. However, there is a lack of research on the formation mechanism of carapace color of this species. This study was conducted to compare the histology and transcriptome in the inner membrane of three carapace color strains of E. sinensis. Histological comparisons revealed that the inner membrane of green and red carapace crabs contained more melanin, appearing in clusters, and had a higher presence of yellow or orange pigments. In contrast, the inner membrane of white carapace crabs had smaller and fewer melanin particles, as well as a lower presence of yellow or orange pigments. Observation under an electron microscope showed that the inner membrane of E. sinensis contained a large number of collagen fibers and various types of cells, including fibroblasts, melanocytes, and other tissue cells, which exhibited different levels of activity. Transcriptome analysis showed that the Green, Red, and White strains of E. sinensis had approximately 80.3 K, 81.6 K and 80.3 K expressed unigenes in their inner membranes, respectively. When comparing Green and Red crabs, there were 2, 850 upregulated genes and 2, 240 downregulated genes. In the comparison between Red and White crabs, there were 2, 853 upregulated genes and 2, 583 downregulated genes. Furthermore, there were 2, 336 upregulated genes and 2, 738 downregulated genes in the inner membranes between White and Green crabs. Among these genes, some members of the solute carriers family, which are involved in carotenoid transportation, showed differential expression among the three carapace color strains. Additionally, significant differences were observed in the expression of genes related to melanin synthesis, including wingless/integrate, tyrosinase, guanine nucleotide-binding protein inhibitory subunit, cell adhesion molecule, adenylyl cyclase, and creb-binding protein. there were no differences in the gene expression levels of the crustacyanin family. In conclusion, this study identified several candidate genes associated with carapace color in the inner membrane of E. sinensis, suggesting a close relationship between the heritable carapace colors and the transport of the carotenoids as well as the synthesis of melanin.

Comparative proteomics elucidates the potential mechanism of heritable carapace color of three strains Chinese mitten crab Eriocheir sinensis

The carapace coloration is important for the environmental adaptation and reproductive behaviors of crustaceans. We selected red, green and white three carapace color strains of Chinese mitten crab (Eriocheir sinensis) strains. These three carapace colors have stable heritability, but the mechanism for their coloration remains unclear.Through histological observations, we have found significant differences in the composition of pigment cells and pigments within the inner membrane of the three color strains, which may be one of the reasons for the color variation. The levels of various carotenoids in both the shell and inner membrane tissues of red and green strains were significantly higher than those of the white strain, while there was no significant difference between the red and green strains. Proteomics studies have identified 2, 034 and 947 different proteins in the shell and inner membrane, respectively. In the shell, there were 18, 13 and 43 differential proteins between red and white strains, green and white strains and green and red strains, respectively. In the inner membrane, there were 44, 24 and 16 differential proteins between red and white strains, green and white strains and green and red strains, respectively. It is clear that the deposited quantity of carotenoids affects the shell formation of three color strains. Some members of the hemocyanin family showed significant variation among different strains. The study yielded two crustacyanin proteins, which were extracted from both the shell and membrane. Of the two proteins, only Crustacyanin-A1 expression showed a difference between the red and green shells strains. In conclusion, these results indicated that the carapace color formation of E. sinensis may be accomplished through pigment binding proteins (PBPs) and pigment cells, which enhance the understanding of color formation mechanism for crustacean.

A natural strategy for astaxanthin stabilization and color regulation: Interaction with proteins

The pigment astaxanthin, one of the carotenoids, is regarded as a functional factor with various biological activities, widely applied in feed, nutraceutical, and cosmetic industries. However, its low stability and poor water solubility limit its application. Examples in nature suggest that binding to proteins is a simple and effective method to improve the stability and bioavailability of astaxanthin. Proteins from algae, fish, and crustaceans have all been demonstrated to have astaxanthin-binding capacity. Inspired by nature, artificial astaxanthin-protein systems have been established in foods. Binding to proteins could bring aquatic species various colors, and changes in the conformation of astaxanthin after binding to proteins leads to color changes. The review innovatively summarizes multiple examples of proteins as means of protecting astaxanthin, giving a reference for exploring and analyzing pigment-protein interactions and providing a strategy for carotenoids stabilization and color regulation, which is beneficial to the broader and deeper applications of carotenoids.

De novo assembly transcriptome analysis reveals the genes associated with body color formation in the freshwater ornamental shrimps Neocaridina denticulate sinensis

The body color of Neocaridina denticulate sinensis is a compelling phenotypic trait, in which a cascade of carotenoid metabolic processes plays an important role. The study was conducted to compare the transcriptome of cephalothoraxes among three pigmentation phenotypes (red, blue, and chocolate) of N. denticulate sinensis. The purpose of this study was to explore the candidate genes associated with different colors of N. denticulate sinensis. Nine cDNA libraries in three groups were constructed from the cephalothoraxes of shrimps. After assembly, 75022 unigenes were obtained in total with an average length of 1026 bp and N50 length of 1876 bp. There were 45977, 25284, 23605, 21913 unigenes annotated in the Nr, Swissprot, KOG, and KEGG databases, respectively. Differential expression analysis revealed that there were 829, 554, and 3194 differentially expressed genes (DEGs) in RD vs BL, RD vs CH, and BL vs CH, respectively. These DEGs may play roles in the absorption, transport, and metabolism of carotenoids. We also emphasized that electron transfer across the inner mitochondrial membrane (IMM) was a key process in pigment metabolism. In addition, a total of 6328 simple sequence repeats (SSRs) were also detected in N. denticulate sinensis. The results laid a solid foundation for further research on the molecular mechanism of integument pigmentation in the crustacean and contributed to developing more attractive aquatic animals.

Transcriptome Analysis Provides Insights into the Mechanism of Astaxanthin Enrichment in a Mutant of the Ridgetail White Prawn Exopalaemon carinicauda

A mutant of the ridgetail white prawn, which exhibited rare orange-red body color with a higher level of free astaxanthin (ASTX) concentration than that in the wild-type prawn, was obtained in our lab. In order to understand the underlying mechanism for the existence of a high level of free astaxanthin, transcriptome analysis was performed to identify the differentially expressed genes (DEGs) between the mutant and wild-type prawns. A total of 78,224 unigenes were obtained, and 1863 were identified as DEGs, in which 902 unigenes showed higher expression levels, while 961 unigenes presented lower expression levels in the mutant in comparison with the wild-type prawns. Based on Gene Ontology analysis and Kyoto Encyclopedia of Genes and Genomes analysis, as well as further investigation of annotated DEGs, we found that the biological processes related to astaxanthin binding, transport, and metabolism presented significant differences between the mutant and the wild-type prawns. Some genes related to these processes, including crustacyanin, apolipoprotein D (ApoD), cathepsin, and cuticle proteins, were identified as DEGs between the two types of prawns. These data may provide important information for us to understand the molecular mechanism of the existence of a high level of free astaxanthin in the prawn.

Expression and function analysis of crustacyanin gene family involved in resistance to heavy metal stress and body color formation in Exopalaemon carinicauda

Crustacyanin has the function of binding astaxanthin which is the best antioxidant, and plays an important role in the body color variation of crustaceans. To investigate the causes of body color variation of the ridgetail white prawn, Exopalaemon carinicauda, the present study obtained four subtypes of crustacyanin gene: C1, C2, A1, and A2. Based on fluorescence quantitative polymerase chain reaction, lipocalin-C1 is mainly expressed in the eyestalk, lipocalin-C2 is in the ventral nerve cord, and lipocalin-A1 and lipocalin-A2 are in subcutaneous adipose tissues. Under the inhibiting effect of Cd²⁺ stress, the expression of four subtypes first increases and then decreases within 24 h, and reaches the maximum at 6 or 12 h. RNA interference experiments showed a decrease in the expression of lipocalin genes in subcutaneous adipose tissue for each subtype, with the body color changing from transparent to red, and the dark red spots on the epidermis changing to bright red. Moreover, the blue protein in the subcutaneous adipose tissue largely disappeared, based on the light micrographs. In view of these findings, the crustacyanin gene appears to fulfill some function in the resistance to heavy metal stress and body color formation of E. carinicauda.

Comparative analysis of transcriptomes from different coloration of Chinese mitten crab Eriocheir sinensis

Chinese mitten crab Eriocheir sinensis is probably the most important freshwater cultured crab in China. A tiny minority of brownish-orange individuals have been discovered in the long period of artificial breeding history of E. sinensiss. Those mutants are usually accompanied with slow growth rate, low molting frequency and poor survival rate, which may be the results of growth defects and immunodeficiency. To better understand the relationship between body color determination and the immune system as well as the related genes expression in E. sinensiss, we performed the whole-body transcriptome analysis in different color of first stage zoea (ZI) larvae using next-generation sequencing (NGS) technology. We randomly assembled 175.40 and 177.52million clean reads from the wild and mutant ZIs, respectively. Finally, we identified 7153 differentially expressed genes (DEGs) (p < 0.05), with 5194 up-regulated and 1959 down-regulated. A total of 13 KEGG pathways related to immune system were detected among 248 pathways. Except the first whole-body RNA sequencing of color-specific transcriptomes for E. sinensis, this study will offer a better understanding of the underlying molecular mechanisms of interaction between color determination and the immune system.

Rapid expansion of pigmentation genes in penaeid shrimp with absolute preservation of function

Crustaceans form their distinct patterns and colours through the interaction of the carotenoid astaxanthin with a protein called crustacyanin (CRCN). Presently, the expression of just two CRCN genes is thought to provide the protein subunits that combine to form the crustacyanin complex and associated carotenoid colour change from red to blue. This study aimed to explore the genetic complexity underlying the production of pigmentation and camouflage in penaeid shrimp. We isolated 35 new CRCN genes from 12 species, and their sequence analysis indicated that this gene family has undergone significant expansion and diversification in this lineage. Despite this duplication and sequence divergence, the structure of the CRCN proteins and their functional role in shrimp colour production has been strictly conserved. Using CRCN isoforms from Penaeus monodon as an example, we showed that isoforms were differentially expressed, and that subtle phenotypes were produced by the specific downregulation of individual isoforms. These findings demonstrate that our knowledge of the molecular basis of pigmentation in shrimp was overly simplistic, and suggests that multiple copies of the CRCN genes within species may be advantageous for colour production. This result is of interest for the origin and evolution of pigmentation in crustaceans, and the mechanisms by which gene function is maintained, diversified or sub-functionalized.

Effect of crude oil petroleum hydrocarbons on protein expression of the prawn Macrobrachium borellii

Hydrocarbon pollution is a major environmental threat to ecosystems in marine and freshwater environments, but its toxicological effect on aquatic organisms remains little studied. A proteomic approach was used to analyze the effect of a freshwater oil spill on the prawn Macrobrachium borellii. To this aim, proteins were extracted from midgut gland (hepatopancreas) of male and female prawns exposed 7 days to a sublethal concentration (0.6 ppm) of water-soluble fraction of crude oil (WSF). Exposure to WSF induced responses at the protein expression level. Two-dimensional gel electrophoresis (2-DE) revealed 10 protein spots that were differentially expressed by WSF exposure. Seven proteins were identified using MS/MS and de novo sequencing. Nm23 oncoprotein, arginine methyltransferase, fatty aldehyde dehydrogenase and glutathione S-transferase were down-regulated, whereas two glyceraldehyde-3-phosphate dehydrogenase isoforms and a lipocalin-like crustacyanin (CTC) were up-regulated after WSF exposure. CTC mRNA levels were further analyzed by quantitative real-time PCR showing an increased expression after WSF exposure. The proteins identified are involved in carbohydrate and amino acid metabolism, detoxification, transport of hydrophobic molecules and cellular homeostasis among others. These results provide evidence for better understanding the toxic mechanisms of hydrocarbons. Moreover, some of these differentially expressed proteins would be employed as potential novel biomarkers.

Structural characterization of recombinant crustacyanin subunits from the lobster Homarus americanus

Crustacean crustacyanin proteins are linked to the production and modification of carapace colour, with direct implications for fitness and survival. Here, the structural and functional properties of the two recombinant crustacyanin subunits H(1) and H(2) from the American lobster Homarus americanus are reported. The two subunits are structurally highly similar to the corresponding natural apo crustacyanin CRTC and CRTA subunits from the European lobster H. gammarus. Reconstitution studies of the recombinant crustacyanin proteins H(1) and H(2) with astaxanthin reproduced the bathochromic shift of 85-95 nm typical of the natural crustacyanin subunits from H. gammarus in complex with astaxanthin. Moreover, correlations between the presence of crustacyanin genes in crustacean species and the resulting carapace colours with the spectral properties of the subunits in complex with astaxanthin confirmed this genotype-phenotype linkage.