Proteomic analysis of ovarian proteins and characterization of thymosin-β and RAC-GTPase activating protein 1 of the giant tiger shrimp Penaeus monodon

Application of proteomics in shrimp and shrimp aquaculture

Since proteins play an important role in the life of an organism, many researchers are now looking at how genes and proteins interact to form different proteins. It is anticipated that the creation of adequate tools for rapid analysis of proteins will accelerate the determination of functional aspects of these biomolecules and develop new biomarkers and therapeutic targets for the diagnosis and treatment of various diseases. Though shrimp contains high-quality marine proteins, there are reports about the heavy losses to the shrimp industry due to the poor quality of shrimp production and many times due to mass mortality also. Frequent outbreaks of diseases, water pollution, and quality of feed are some of the most recognized reasons for such losses. In the seafood export market, shrimp occupies the top position in currency earnings and strengthens the economy of many developing nations. Therefore, it is vital for shrimp-producing companies they produce healthy shrimp with high-quality protein. Though aquaculture is a very competitive market, global awareness regarding the use of scientific knowledge and emerging technologies to obtain better-farmed organisms through sustainable production has enhanced the importance of proteomics in seafood biology research. Proteomics, as a powerful tool, has therefore been increasingly used to address several issues in shrimp aquaculture. In the present paper, efforts have been made to address some of them, particularly the role of proteomics in reproduction, breeding and spawning, immunological responses and disease resistance capacity, nutrition and health, microbiome and probiotics, quality and safety of shrimp production, bioinformatics applications in proteomics, the discovery of protein biomarkers, and mitigating biotic and abiotic stresses. Future challenges and research directions on proteomics in shrimp aquaculture have also been discussed.

Thymosins participate in antibacterial immunity of kuruma shrimp, Marsupenaeus japonicus

Thymosins β are actin-binding proteins that play a variety of different functions in inflammatory responses, wound healing, cell migration, angiogenesis, and stem cell recruitment and differentiation. In crayfish, thymosins participate in antiviral immunology. However, the roles of thymosin during bacterial infection in shrimp remain unclear. In the present study, four thymosins were identified from kuruma shrimp, Marsupenaeus japonicus, and named as Mjthymosin2, Mjthymosin3, Mjthymosin4, and Mjthymosin5 according the number of their thymosin beta actin-binding motifs. Mjthymosin3 was selected for further study because its expression level was the highest in hemocytes. Expression analysis showed that Mjthymosin3 was upregulated in hemocytes after challenged by Vibrio anguillarum or Staphylococcus aureus. The recombinant Mjthymosin3 protein could inhibit the growth of certain bacteria in an in vitro antibacterial test. Mjthymosins could facilitate external bacterial clearance in shrimp, and were beneficial to shrimp survival post V. anguillarum or S. aureus infection. The results suggested that Mjthymosins played important roles in the antibacterial immune response of kuruma shrimp.

A proteomic insight into vitellogenesis during tick ovary maturation

Ticks are arthropod ectoparasites of importance for public and veterinary health. The understanding of tick oogenesis and embryogenesis could contribute to the development of novel control methods. However, to date, studies on the temporal dynamics of proteins during ovary development were not reported. In the present study we followed protein profile during ovary maturation. Proteomic analysis of ovary extracts was performed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) using shotgun strategy, in addition to dimethyl labelling-based protein quantification. A total of 3,756 proteins were identified, which were functionally annotated into 30 categories. Circa 80% of the annotated proteins belong to categories related to basal metabolism, such as protein synthesis and modification machineries, nuclear regulation, cytoskeleton, proteasome machinery, transcriptional machinery, energetic metabolism, extracellular matrix/cell adhesion, immunity, oxidation/detoxification metabolism, signal transduction, and storage. The abundance of selected proteins involved in yolk uptake and degradation, as well as vitellin accumulation during ovary maturation, was assessed using dimethyl-labelling quantification. In conclusion, proteins identified in this study provide a framework for future studies to elucidate tick development and validate candidate targets for novel control methods.

Top-Down Proteomics and Farm Animal and Aquatic Sciences

Proteomics is a field of growing importance in animal and aquatic sciences. Similar to other proteomic approaches, top-down proteomics is slowly making its way within the vast array of proteomic approaches that researchers have access to. This opinion and mini-review article is dedicated to top-down proteomics and how its use can be of importance to animal and aquatic sciences. Herein, we include an overview of the principles of top-down proteomics and how it differs regarding other more commonly used proteomic methods, especially bottom-up proteomics. In addition, we provide relevant sections on how the approach was or can be used as a research tool and conclude with our opinions of future use in animal and aquatic sciences.

The Rho GTPase Family Genes in Bivalvia Genomes: Sequence, Evolution and Expression Analysis

Background

Rho GTPases are important members of the Ras superfamily, which represents the largest signaling protein family in eukaryotes, and function as key molecular switches in converting and amplifying external signals into cellular responses. Although numerous analyses of Rho family genes have been reported, including their functions and evolution, a systematic analysis of this family has not been performed in Mollusca or in Bivalvia, one of the most important classes of Mollusca.

Results

In this study, we systematically identified and characterized a total set (Rho, Rac, Mig, Cdc42, Tc10, Rnd, RhoU, RhoBTB and Miro) of thirty Rho GTPase genes in three bivalve species, including nine in the Yesso scallop Patinopecten yessoensis, nine in the Zhikong scallop Chlamys farreri, and twelve in the Pacific oyster Crassostrea gigas. Phylogenetic analysis and interspecies comparison indicated that bivalves might possess the most complete types of Rho genes in invertebrates. A multiple RNA-seq dataset was used to investigate the expression profiles of bivalve Rho genes, revealing that the examined scallops share more similar Rho expression patterns than the oyster, whereas more Rho mRNAs are expressed in C. farreri and C. gigas than in P. yessoensis. Additionally, Rho, Rac and Cdc42 were found to be duplicated in the oyster but not in the scallops. Among the expanded Rho genes of C. gigas, duplication pairs with high synonymous substitution rates (Ks) displayed greater differences in expression.

Conclusion

A comprehensive analysis of bivalve Rho GTPase family genes was performed in scallop and oyster species, and Rho genes in bivalves exhibit greater conservation than those in any other invertebrate. This is the first study focusing on a genome-wide characterization of Rho GTPase genes in bivalves, and the findings will provide a valuable resource for a better understanding of Rho evolution and Rho GTPase function in Bivalvia.

Gonadal transcriptomic analysis and differentially expressed genes in the testis and ovary of the Pacific white shrimp (Litopenaeus vannamei)

Background

The Pacific white shrimp (Litopenaeus vannamei) is the world’s most prevalent cultured crustacean species. However, the supply of high-quality broodstocks is limited and baseline information related to its reproductive activity and molecular issues related to gonad development are scarce. In this study, we performed transcriptome sequencing on the gonads of adult male and female L. vannamei to identify sex-related genes.

Results

A total of 25.16 gigabases (Gb) of sequences were generated from four L. vannamei gonadal tissue libraries. After quality control, 24.11 Gb of clean reads were selected from the gonadal libraries. De-novo assembly of all the clean reads generated a total of 65,218 unigenes with a mean size of 1021 bp and a N50 of 2000 bp. A search of all-unigene against Nr, SwissProt, KEGG, COG and NT databases resulted in 26,482, 23,062, 20,659, 11,935 and 14,626 annotations, respectively, providing a total of 30,304 annotated unigenes. Among annotated unigenes, 12,320 unigenes were assigned to gene ontology categories and 20,659 unigenes were mapped to 258 KEGG pathways. By comparing the ovary and testis libraries, 19,279 testicular up-regulated and 3,529 ovarian up-regulated unigenes were identified. Enrichment analysis of differentially expressed unigenes resulted in 1060 significantly enriched GO terms and 34 significantly enriched KEGG pathways. Nine ovary-specific, 6 testis-specific, 45 testicular up-regulated and 39 ovarian up-regulated unigenes were then confirmed by semi-quantitative PCR and quantitative real-time PCR. In addition, using all-unigenes as a reference, a total of 13,233 simple sequence repeats (SSRs) were identified in 10,411 unigene sequences.

Conclusions

The present study depicts the first large-scale RNA sequencing of shrimp gonads. We have identified many important sex-related functional genes, GO terms and pathways, all of which will facilitate future research into the reproductive biology of shrimp. We expect that the SSRs detected in this study can then be used as genetic markers for germplasm evaluation of breeding and imported populations.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-2219-4) contains supplementary material, which is available to authorized users.

A Rac1 GTPase is a critical factor in the immune response of shrimp (Litopenaeus vannamei) to Vibrio alginolyticus infection

The small GTPase Rac1 acts as a molecular switch for signal transduction that regulates various cellular functions. However, its functions in crustaceans remain unclear. In this study, a cDNA encoding a RAS GTPase (LvRac1) in the Pacific white shrimp (L. vannamei) was identified and characterized. A recombinant variant of this GTPase, rLvRac1, was expressed in the model organism P. pastoris and its expression was confirmed by mass spectrometry. Biochemical assays indicated that the recombinant protein retained GTPase activity and was expressed in all of the organism's tested tissues. Injection of the bacterium V. alginolyticus into L. vannamei induced hepatopancreatic upregulation of LvRac1 expression. Moreover, knocking down LvRac1 in vivo significantly reduced the expression of the L. vannamei p53 and Cu/Zn superoxide dismutase genes (Lvp53 and LvCu/Zn SOD, respectively) while increasing that of the galectin gene (Lvgal). Hemolymph samples from control and LvRac1-silenced L. vannamei individuals were analyzed by flow cytometry, revealing that the latter exhibited significantly reduced respiratory burst activity and total hemocyte counts. Cumulative mortality in shrimp lacking LvRac1 was significantly greater than in control groups following V. alginolyticus challenge. The silencing of LvRac1 by double-stranded RNA injection thus increased the V. alginolyticus challenge sensitivity of L. vannamei and weakened its bacterial clearance ability in vivo. Suppressing LvRac1 also promoted the upregulation of Lvp53, LvCu/ZnSOD, and Lvgal following V. alginolyticus injection. Taken together, these results suggest that LvRac1 is important in the innate immune response of shrimp to V. alginolyticus infection.