Abstract
The swimming crab Portunus trituberculatus is an economically important marine crustacean species. Here isobaric tags for relative and absolute quantitation (iTRAQ) analysis were used to identify proteins that are differentially expressed during larval development of P. trituberculatus to elucidate the underlying mechanisms. In comparison with the first zoea stage (Z1), 3980 proteins were identified from 32789 peptides, which were matched with 115497 spectrums. A total of 241 proteins were screened with significantly differential expressions in all development stages. These 241 proteins are involved in various biological processes, such as cytoskeleton organization, protein synthesis, energy production and substance metabolism, physiological activities, and transport. Cluster analyses of the 241 differentially expressed proteins led to the generation of four protein clusters based on the overall similarity in protein expression patterns. Exactly 54, 70, 36, and 45 proteins clustered in profiles 10 (0, 0, 0, −1, 0, 0), 15 (0, 1, 0, 1, 0, 1), 18 (0, 1, 2, 2, 1, 0), and 19 (0, 1, 2, 3, 4, 5), respectively. Muscle development and exoskeleton renewal were important processes throughout the development stages. In addition, protein synthesis, degradation, and digestion actively occurred, especially at the Z4 stage. These results provide novel insights into the mechanisms underlying larval development of swimming crab and can assist in larval rearing.
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Andersen, G. R., Nissen, P., and Nyborg, J., 2003. Elongation factors in protein biosynthesis. Trends in Biochemical Sciences, 28(8): 434–441.
Bérubé, N. G., 2011. ATRX in chromatin assembly and genome architecture during development and disease. Biochemistry and Cell Biology, 89(5): 435–444.
Bradford, M. M., 1976. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Analytical Biochemistry, 72(1–2): 248–254.
Burmester, T., 1999. Identification, molecular cloning, and phylogenetic analysis of a non-respiratory pseudo-hemocyanin of Homarus americanus. Journal of Biological Chemistry, 274(19): 13217–13222.
Burmester, T., 2002. Origin and evolution of arthropod hemocyanins and related proteins. Journal of Comparative Physiology B, 172(2): 95–107.
Cardoso, C., Couillault, C., Mignon-Ravix, C., Millet, A., Ewbank, J. J., Fontés, M., et al., 2005. XNP-1/ATR-X acts with RB, HP1 and the NuRD complex during larval development in C. elegans. Developmental Biology, 278(1): 49–59.
Charles, J. P., 2010. The regulation of expression of insect cuticle protein genes. Insect Biochemistry Molecular Biology, 40(3): 205–213.
Chinopoulos, C., and Adam-Vizi, V., 2009. Mitochondria as ATP consumers in cellular pathology. Biochimica et Biophysica Acta, 1802(1): 221–227.
Dan, S., Ashidate, M., and Hamasaki, K., 2016. Improved method for culturing the swimming crab Portunus trituberculatus larvae to prevent mass mortality during seed production. Fisheries Science, 82(1): 113–126.
Dan, S., Kaneko, T., Takeshima, S., Ashidate, M., and Hamasaki, K., 2014. Eyestalk ablation affects larval morphogenesis in the swimming crab Portunus trituberculatus during metamorphosis into megalopae. Sexuality and Early Development in Aquatic Organisms, 1(1): 57–73.
Dan, S., Oshiro, M., Ashidate, M., and Hamasaki, K., 2016. Starvation of Artemia in larval rearing water affects post-larval survival and morphology of the swimming crab, Portunus trituberculatus (Brachyura, Portunidae). Aquaculture, 452: 407–415.
Decker, H., and Jaenicke, E., 2004. Recent findings on phenoloxidase activity and antimicrobial activity of hemocyanins. Developmental and Comparative Immunology, 28: 673–687.
Duan, Y., Li, J., Zhang, Z., Li, J., and Liu, P., 2016. Characterization of ADP ribosylation factor 1 gene from Exopalaemon carinicauda and its immune response to pathogens challenge and ammonia-N stress. Fish & Shellfish Immunology, 55: 123–130.
Feder, M. E., and Walser, J. C., 2005. The biological limitations of transcriptomics in elucidating stress and stress responses. Journal of Evolutionary Biology, 18(4): 901–910.
Fu, Y., Zhu, F., Liu, L., Lu, S., Ren, Z., Mu, C., et al., 2018. iTRAQ-based proteomic analysis identifies proteins involved in limb regeneration of swimming crab Portunus trituberculatus. Comparative Biochemistry and Physiology Part D, 26: 10–19.
Fujieda, N., Yakiyama, A., and Itoh, S., 2019. Five monomeric hemocyanin subunits from Portunus trituberculatus: Purification, spectroscopic characterization, and quantitative evaluation of phenol monooxygenase activity. Biochimica et Biophysica Acta, 1804(11): 2128–2135.
Han, F., and Zhang, X., 2007. Characterization of a ras-related nuclear protein (Ran protein) up-regulated in shrimp antiviral immunity. Fish & Shellfish Immunology, 23: 937–944.
Hu, A. S., 1958. Glucose metabolism in the crab, Hemigrapsus nudus. Archives of Biochemistry and Biophysics, 5(2): 387–395.
Huan, P., Wang, H., Dong, B., and Liu, B., 2012. Identification of differentially expressed proteins involved in the early larval development of the Pacific oyster Crassostrea gigas. Journal of Proteomics, 75(13): 3855–3865.
Jäkel, S., and Görlich, D., 1998. Importin beta, transportin, RanBP5 and RanBP7 mediate nuclear import of ribosomal proteins in mammalian cells. The EMBO Journal, 17(15): 4491–4502.
Johnston, D. J., 2003. Ontogenetic changes in digestive enzyme activity of the spiny lobster, Jasus edwardsii (Decapoda; Palinuridae). Marine Biology, 143(6): 1071–1082.
Jung, H., Lyons, R. E., Hurwood, D. A., and Mather, P. B., 2013. Genes and growth performance in crustacean species: A review of relevant genomic studies in crustaceans and other taxa. Reviews in Aquaculture, 5(2): 77–110.
Kallapur, V. L., Ramamohanrao, Y., and Narasubhai, A. V., 1983. Glycolytic enzymes in the premolt field crab Paratelphusa hydrodromus (Milne-Edwards) (Crustacea). Archives Internationales de Physiologie et de Biochimie, 91(2): 127–132.
Kamimura, M. T., Meier, K. M., Cavalli, R. O., Laurino, J., Maggioni, R., and Marins, L. F., 2008. Characterization of growth-related genes in the south-western Atlantic pink shrimp Farfantepenaeus paulensis (Pérez-Farfante 1967) through a modified DDRT-PCR protocol. Aquaculture Research, 39(2): 200–204.
Karouzou, M. V., Spyropoulos, Y., Iconomidou, V. A., Cornman, R. S., Hamodrakas, S. J., and Willis, J. H., 2007. Drosophila cuticular proteins with the R&R consensus: Annotation and classification with a new tool for discriminating RR-1 and RR-2 sequences. Insect Biochemistry and Molecular Biology, 37(8): 754–760.
Kuballa, A. V., Merritt, D. J., and Elizur, A., 2007. Gene expression profiling of cuticular proteins across the moult cycle of the crab Portunus pelagicus. BMC Biology, 5(1): 45.
Labriet, A., Lévesque, É., Cecchin, E., De Mattia, E., Villeneuve, L., Rouleau, M., et al., 2019. Germline variability and tumor expression level of ribosomal protein gene RPL28 are associated with survival of metastatic colorectal cancer patients. Scientific Reports, 9(1): 13008.
Larsson, O., Tian, B., and Sonenberg, N., 2013. Toward a genome-wide landscape of translational control. Cold Spring Harbor Perspectives in Biology, 5(1): a012302.
Li, J., Li, H., Zhang, Z., and Pan, Y., 2007. Identification of the proteome complement of high royal jelly producing bees (Apis mellifera) during worker larval development. Apidologie, 38(6): 545–557.
Li, Y., Hui, M., Cui, Z., Liu, Y., Song, C., and Shi, G., 2015. Comparative transcriptomic analysis provides insights into the molecular basis of the metamorphosis and nutrition metabolism change from zoeae to megalopae in Eriocheir sinensis. Comparative Biochemistry and Physiology Part D, 13: 1–9.
Livak, K. J., and Schmittgen, T. D., 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods, 25(4): 402–408.
McDowell, T. L., Gibbons, R. J., Sutherland, H., O’Rourke, D. M., Bickmore, W. A., Pombo, A., et al., 1999. Localization of a putative transcriptional regulator (ATRX) at pericentromeric heterochromatin and the short arms of acrocentric chromosomes. Proceedings of the National Academy of Sciences, 96(24): 13983–13988.
Morioka, Y., Kitajima, C., and Hayashida, G., 1988. Oxygen consumption, growth and calculated food requirement of the swimming crab Portunus Trituberculatus in its early developmental stage. Nippon Suisan Gakkaishi, 54(7): 1137–1141.
Nagamatsu, Y., Yanagisawa, I., Kimoto, M., Okamoto, E., and Koga, D., 1995. Purification of a chitooligosaccharidolytic β-N-acetylglucosaminidase from Bombyx mori larvae during metamorphosis and the nucleotide sequence of its cDNA. Bioscience, Biotechnology, and Biochemistry, 59(2): 219–225.
Pan, L. Q., Xiao, G. Q., Zhang, H. X., and Luan, Z. H., 2005. Effects of different dietary protein content on growth and protease activity Eriocheir sinensis larvae. Aquaculture, 246(1–4): 313–319.
Pandey, A., and Mann, M., 2000. Proteomics to study genes and genomes. Nature, 405(6788): 837–846.
Park, M. H., 2006. The post-translational synthesis of a polyamine-derived amino acid, hypusine, in the eukaryotic translation initiation factor 5A (eIF5A). Journal of Biochemistry, 139: 161–169.
Peng, H., Zhao, Y., Chen, J., Huo, J., Zhang, Y., and Xiao, T., 2019. Knockdown of ribosomal protein S3 causes preimplantation developmental arrest in mice. Theriogenology, 129: 77–81.
Peters, G., Saborowski, R., Buchholz, F., and Mentlein, R., 1999. Two distinct forms of the chitin-degrading enzyme N-acetyl-β-d-glucosaminidase in the Antarctic krill: Specialists in digestion and moult. Marine Biology, 134(4): 697–703.
Pierce, A., Unwin, R. D., Evans, C. A., Griffiths, S., Carney, L., Zhang, L., et al., 2008. Eight-channel iTRAQ enables comparison of the activity of six leukemogenic tyrosine kinases. Molecular & Cellular Proteomics, 7(5): 853–863.
Ramakrishnan, V., 2011. The eukaryotic ribosome. Science, 331(6018): 681–682.
Ren, Q., and Pan, L., 2014. Digital gene expression analysis in the gills of the swimming crab (Portunus trituberculatus) exposed to elevated ambient ammonia-N. Aquaculture, 434: 108–114.
Ren, X., Wang, Z., Gao, B., Liu, P., and Li, J., 2017. Toxic responses of swimming crab (Portunus trituberculatus) larvae exposed to environmentally realistic concentrations of oxytetracycline. Chemosphere, 173: 563–571.
Rui, Y., Bai, J., and Perrimon, N., 2010. Sarcomere formation occurs by the assembly of multiple latent protein complexes. PLoS Genet, 6(11): e1001208.
Schweitzer, A., Aufderheide, A., Rudack, T., Beck, F., Pfeifer, G., Plitzko, J. M., et al., 2016. Structure of the human 26S proteasome at a resolution of 3.9 Å. Proceedings of the National Academy of Sciences, 113(28): 7816–7821.
Soares, M. P., Silva-Torres, F. A., Elias-Neto, M., Nunes, F. M., Simoes, Z. L., and Bitondi, M. M., 2011. Ecdysteroid-dependent expression of the tweedle and peroxidase genes during adult cuticle formation in the honey bee, Apis mellifera. PLoS One, 6(5): e20513.
Sveinsdóttir, H., Vilhelmsson, O., and Gudmundsdóttir, Á., 2008. Proteome analysis of abundant proteins in two age groups of early Atlantic cod (Gadus morhua) larvae. Comparative Biochemistry and Physiology Part D, 3: 243–250.
Stenmark, H., and Olkkonen, V. M., 2001. The Rab GTPase family. Genome Biology, 2(5): REVIEWS3007.
Togawa, T., Dunn, W. A., Emmons, A. C., Nagao, J., and Willis, J. H., 2008. Developmental expression patterns of cuticular protein genes with the R&R Consensus from Anopheles gambiae. Insect Biochemistry and Molecular Biology, 38(5): 508–519.
Trinick, J., and Tskhovrebova, L., 1999. Titin: A molecular control freak. Trends in Biochemical Sciences, 9(10): 377–380.
Unwin, R. D., Griffiths, J. R., and Whetton, A. D., 2010. Simultaneous analysis of relative protein expression levels across multiple samples using iTRAQ isobaric tags with 2D nano LC-MS/MS. Nature Protocols, 5(9): 1574–1582.
Wang, C., Jiang, L., Wang, R., and Li, Y., 2010. Effect of abrupt and gradual changes in salinity on development and feeding in juvenile swimming crab (Portunus trituberculatus). Fisheries Science, 29(9): 510–514 (in Chinese with English abstract).
Wang, J., Li, J., Kang, K., and Cheng, Y., 2004. Effects of water temperature and photoperiod on survival, and metamorphosis of Portunns tritubuculatus larvae. Journal of Beijing Fisheries, 1: 8–10 (in Chinese with English abstract).
Wei, J., Zhang, X., Yu, Y., Huang, H., Li, F., and Xiang, J., 2014. Comparative transcriptomic characterization of the early development in Pacific white shrimp Litopenaeus vannamei. PLoS One, 9: e106201.
Wu, X., Zeng, C. C., and Southgate, P., 2014. Ontogenetic patterns of growth and lipid composition changes of blue swimmer crab larvae: Insights into larval biology and lipid nutrition. Marine and Freshwater Ressearch, 65(3): 228–243.
Xu, J., Wang, C., Mu, C., and Zhang, L., 2012. Relationship between oxygen consumption and oxygen consumption rate and the body mass of Portunus trituberculatus at its early development stages. Journal of Marine Science, 30(1): 102–106 (in Chinese with English abstract).
Xu, Q., Liu, R., and Liu, Y., 2009. Genetic population structure of the swimming crab, Portunus trituberculatus in the East China Sea based on mtDNA 16S rRNA sequences. Journal of Experimental Marine Biology and Ecology, 371(2): 121–129.
Yasunobu, H., Nagayama, H., Nakamura, K., and Hatai, K., 1997. Prevention of a fungal infection in the swimming crab Portunus trituberculatus larvae by high pH of rearing water. Nippon Suisan Gakkaishi, 63(1): 56–63.
Zhang, Y., Fonslow, B. R., Shan, B., Baek, M. C., and Yates 3rd, J. R., 2013. Protein analysis by shotgun/bottom-up proteomics. Chemical Review, 113: 2343–2394.
Zhang, Y., Dong, Z., Wang, D., Wu, Y., Song, Q., Gu, P., et al., 2014. Proteomics of larval hemolymph in Bombyx mori reveals various nutrient-storage and immunity-related proteins. Amino Acids, 46(4): 1021–1031.
Acknowledgements
We thank members of our laboratory for their stimulating discussion and helpful comments on this manuscript. This work was supported by the National Natural Science Foundation of China (No. 41676140), the Major Agriculture Program of Ningbo (No. 2017C110007), the Modern Technology System of Agricultural Industry (No. CARS-48), and the K C Wong Magana Fund in Ningbo University.
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Chen, X., Mu, C., Li, R. et al. Using iTRAQ-Based Quantitative Proteomics Analysis to Identify Differentially Expressed Proteins Related to Larval Development of Portunus trituberculatus. J. Ocean Univ. China 20, 897–910 (2021). https://doi.org/10.1007/s11802-021-4649-8
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DOI: https://doi.org/10.1007/s11802-021-4649-8