Abstract
Environmental salinity is an important abiotic factor influencing normal physiological functions and productive performance in the sea cucumber Apostichopus japonicus. It is therefore important to understand how changes in salinity affect sea cucumbers in the face of global climate change. In this study, we investigated the responses to salinity stress in sea cucumbers using mRNA and miRNA sequencing. The regulatory network of mRNAs and miRNAs involved in salinity stress was examined, and the metabolic pathways enriched for differentially expressed miRNAs and target mRNAs were identified. The top 20 pathways were involved in carbohydrate metabolism, fatty acid metabolism, degradation, and elongation, amino acid metabolism, genetic information processing, metabolism of cofactors and vitamins, transport and catabolism, and environmental information processing. A total of 22 miRNAs showed differential expression during salinity acclimation. The predicted 134 target genes were enriched in functions consistent with the results of gene enrichment based on transcriptome analysis. These results suggested that sea cucumbers deal with salinity stress via changes in amino acid metabolism, ion channels, transporters, and aquaporins, under stimulation by environmental signals, and that this process requires energy from carbohydrate and fatty acid metabolism. Salinity challenge also induced miRNA expression. These results provide a valuable genomic resource that extends our understanding of the unique biological characteristics of this economically important species under conditions of salinity stress.
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Asha PS, Muthiah P (2005) Effects of temperature, salinity and pH on larval growth, survival and development of the sea cucumber Holothuria spinifera Theel. Aquaculture 250(3–4):823–829
Berger VJ, Kharazova AD (1997) Mechanisms of salinity adaptations in marine molluscs. In interactions and adaptation strategies of marine organisms. Springer, Dordrecht, pp 115–126
Beyenbach KW, Wieczorek H (2006) The V-type H+ ATPase: molecular structure and function, physiological roles and regulation. J Exp Biol 209(4):577–589
Bradbury MW (2006) Lipid metabolism and liver inflammation. I Hepatic fatty acid uptake: possible role in steatosis. Am J Physiol-Gastr L 290(2):194–198
Breves JP, Fox BK, Pierce AL, Hirano T, Grau EG (2010) Gene expression of growth hormone family and glucocorticoid receptors, osmosensors, and ion transporters in the gill during seawater acclimation of Mozambique tilapia, Oreochromis mossambicus. J Exp Zool A 313(7):432–441
Chaney ML, Gracey AY (2011) Mass mortality in Pacific oysters is associated with a specific gene expression signature. Mol Ecol 20(14):2942–2954
Chen K, Li E, Li T, Xu C, Wang X, Lin H, Qin JG, Chen LQ (2015) Transcriptome and molecular pathway analysis of the hepatopancreas in the Pacific white shrimp Litopenaeus vannamei under chronic low-salinity stress. PLoS One 10:e0131503
Chow SC, Ching LY, Wong AMF, Wong CK (2009) Cloning and regulation of expression of the Na+–Cl––taurine transporter in gill cells of freshwater Japanese eels. J Exp Biol 212(20):3205–3210
Corporeau C, Tamayo D, Pernet F, Quéré C, Madec S (2014) Proteomic signatures of the oyster metabolic response to herpesvirus OsHV-1μVar infection. J Proteome 109:176–187
DeZoysa M, Whang I, Lee Y, Lee S, Lee JS, Lee J (2009) Transcriptional analysis of antioxidant and immune defense genes in disk abalone (Haliotis discus discus) during thermal, low-salinity and hypoxic stress. Comp Biochem Physiol B 154(4):387–395
Diehl WJ (1986) Osmoregulation in echinoderms. Comp Biochem Phys A 84(2):199–205
Dietz KJ, Tavakoli N, Kluge C, Mimura T, Sharma SS, Harris GC, Chardonnens AN, Golldack D (2001) Significance of the V-type ATPase for the adaptation to stressful growth conditions and its regulation on the molecular and biochemical level. J Exp Bot 52(363):1969–1980
Dong Y, Dong S, Meng X (2008) Effects of thermal and osmotic stress on growth, osmoregulation and Hsp70 in sea cucumber (Apostichopus japonicus Selenka). Aquaculture 276:179–186
Evans DH, Piermarini PM, Choe KP (2005) The multifunctional fish gill: dominant site of gas exchange osmoregulation, acid-base regulation, and excretion of nitrogenous waste. Physiol Rev 85(1):97–177
Evans DH, Claiborne JB (2006) The physiology of fishes.CRC
Evans TG (2010) Co-ordination of osmotic stress responses through osmosensing and signal transduction events in fishes. J Fish Biol 76(8):1903–1925
Fiess JC, Kunkel-Patterson A, Mathias L, Riley LG, Yancey PH, Hirano T, Grau EG (2007) Effects of environmental salinity and temperature on osmoregulatory ability, organic osmolytes, and plasma hormone profiles in the Mozambique tilapia (Oreochromis mossambicus). Comp Biochem Phys A 146(2):252–264
Flynt AS, Thatcher EJ, Burkewitz K, Li N, Liu Y, Patton JG (2009) miR-8 microRNAs regulate the response to osmotic stress in zebrafish embryos. J Cell Boil 185(1):115–127
Friedländer MR, Mackowiak SD, Li N, et al. (2011) miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. J Nucleic Acids Res 40(1):37–52
Gao W, Tan B, Mai K, Chi S, Liu H, Dong X, Yang Q (2012) Profiling of differentially expressed genes in hepatopancreas of white shrimp (Litopenaeus vannamei) exposed to long-term low salinity stress. Aquaculture 364:186–191
Godi A, DiCampli A, Konstantakopoulos A, DiTullio G, Alessi DR, Kular GS, Daniele T, Marra P, Lucocq JM, DeMatteis MA (2004) FAPPs control Golgi-to-cell-surface membrane traffic by binding to ARF and PtdIns (4) P. Nat Cell Boil 6(5):393
Greenberg AS, McDaniel ML (2002) Identifying the links between obesity, insulin resistance and β-cell function: potential role of adipocyte-derived cytokines in the pathogenesis of type 2 diabetes. Eur J Clin Investig 32:24–34
Gu XH, Jiang DL, Huang Y, Li BJ, Chen CH, Lin HR, Xia JH (2018) The sea cucumber Holothuria scabra in Nile Tilapia using QTL-Seq. Mar Biotechnol:1–10
Hamel JF, Conand C, Pawson DL, Mercier A (2001) The sea cucumber Holothuria scabra (Holothuroidea: Echinodermata): its biology and exploitation as beche-de-mer:129–223
Hediger MA, Romero MF, Peng JB, Rolfs A, Takanaga H, Bruford EA (2004) The ABCs of solute carriers: physiological, pathological and therapeutic implications of human membrane transport proteins. Pflugers Arch 447(5):465–468
Hui M, Liu Y, Song C, Li Y, Shi G, Cui Z (2014) Transcriptome changes in Eriocheir sinensis megalopae after desalination provide insights into osmoregulation and stress adaption in larvae. PLoS One 9(12):e114187
Huo D, Sun L, Li X, Ru X, Liu S, Zhang L, Yang H (2017) Differential expression of miRNAs in the respiratory tree of the sea cucumber Apostichopus japonicus under hypoxia stress. G3 7(11):3681–3692
Ivanina AV, Froelich B, Williams T, Sokolov EP, Oliver JD, Sokolova IM (2011) Interactive effects of cadmium and hypoxia on metabolic responses and bacterial loads of eastern oysters Crassostrea virginica Gmelin. Chemosphere 82(3):377–389
Jeong SY, Kim JH, Lee WO, Dahms HU, Han KN (2014) Salinity changes in the anadromous river pufferfish, Takifugu obscurus, mediate gene regulation. Fish Physiol Biochem 40(1):205–219
Kashenko SD (2000) Acclimation of the sea cucumber Apostichopus japonicus to decreased salinity at the blastula and gastrula stages: its effect on the desalination resistance of larvae at subsequent stages of development. Russ J Mar Biol 26(6):422–426
Kim YK, Jang SK (2002) Continuous heat shock enhances translational initiation directed by internal ribosomal entry site. Biochem Biophys Res Commun 297(2):224–231
Koepsell H (2013) The SLC22 family with transporters of organic cations, anions and zwitterions. Mol Asp Med 34(2–3):413–435
Langmead B, Trapnell C, Pop M, et al. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. J Gen Biol 10(3):25
Lansdell SJ, Gee VJ, Harkness PC, Doward AI, Baker ER, Gibb AJ, Millar NS (2005) RIC-3 enhances functional expression of multiple nicotinic acetylcholine receptor subtypes in mammalian cells. Mol Pharmacol
Li E, Wang S, Li C, Wang X, Chen K, Chen L (2014) Transcriptome sequencing revealed the genes and pathways involved in salinity stress of Chinese mitten crab, Eriocheir sinensis. Physiol Genomics 46(5):177–190
Li L, Li Q (2010) Effects of stocking density temperature, and salinity on larval survival and growth of the red race of the sea cucumber Apostichopus japonicus (Selenka). Aquac Int 18(3):447–460
Lustig B, Jerchow B, Sachs M, Weiler S, Pietsch T, Karsten U, Wetering M, Clevers H, Schlag PM, Birchmeier W, Behrens J (2002) Negative feedback loop of Wnt signaling through upregulation of conductin/axin2 in colorectal and liver tumors. Mol Cell Biol 22(4):1184–1193
Lv J, Liu P, Gao B, Li J (2016) The identification and characteristics of salinity-related microRNAs in gills of Portunus trituberculatus. Cell Stress Chaperones 21(1):63–74
Lv J, Liu P, Wang Y, Gao B, Chen P, Li J (2013) Transcriptome analysis of Portunus trituberculatus in response to salinity stress provides insights into the molecular basis of osmoregulation. PLoS One 8(12):e82155
Marshall WS, Watters KD, Hovdestad LR, Cozzi RR, Katoh F (2009) CFTR Cl–channel functional regulation by phosphorylation of focal adhesion kinase at tyrosine 407 in osmosensitive ion transporting mitochondria rich cells of euryhaline killifish. J Exp Biol 212(15):2365–2377
McCormick SD (2001) Endocrine control of osmoregulation in teleost fish. Am Zool 41(4):781–794
Meng J, Zhu Q, Zhang L, Li C, Li L, She Z, Zhang G (2013) Genome and transcriptome analyses provide insight into the euryhaline adaptation mechanism of Crassostrea gigas. PLoS One 8(3):e58563
Mihaljevic I, Popovic M, Zaja R, Smital T (2016) Phylogenetic, syntenic, and tissue expression analysis of slc22 genes in zebrafish (Danio rerio). BMC Genomics 17(1):626
Milan M, Coppe A, Reinhardt R, Cancela LM, Leite RB, Saavedra C, Bargelloni L (2011) Transcriptome sequencing and microarray development for the Manila clam, Ruditapes philippinarum: genomic tools for environmental monitoring. BMC Genomics 12(1):234
Nie H, Jiang L, Chen P, Huo Z, Yang F, Yan X (2017) High throughput sequencing of RNA transcriptomes in Ruditapes philippinarum identifies genes involved in osmotic stress response. Sci Rep-UK 7(1):4953
Ouattara NG, Bodinier C, Nègre-Sadargues G, D'Cotta H, Messad S, Charmantier G, Panfili J, Baroiller JF (2009) Changes in gill ionocyte morphology and function following transfer from fresh to hypersaline waters in the tilapia Sarotherodon melanotheron. Aquaculture 290(1–2):155–164
Palacios E, Bonilla A, Luna D, Racotta IS (2004a) Survival, Na+/K+-ATPase and lipid responses to salinity challenge in fed and starved white pacific shrimp (Litopenaeus vannamei) postlarvae. Aquaculture 234(1–4):497–511
Palacios E, Bonilla A, Pérez A, Racotta IS, Civera R (2004b) Influence of highly unsaturated fatty acids on the responses of white shrimp (Litopenaeus vannamei) postlarvae to low salinity. J Exp Mar Biol Ecol 299(2):201–215
Parsons JT, Martin KH, Slack JK, Taylor JM, Weed SA (2000) Focal adhesion kinase: a regulator of focal adhesion dynamics and cell movement. Oncogene 19(49):5606
Paulsen CE, Armache JP, Gao Y, Cheng Y, Julius D (2015) Structure of the TRPA1 ion channel suggests regulatory mechanisms. Nature 520(7548):511
Ranallo RF, Rhodes EC (1998) Lipid metabolism during exercise. Sports Med 26(1):29–42
Rastorguev SM, Nedoluzhko AV, Sharko FS, Boulygina ES, Sokolov AS, Gruzdeva NM, Prokhortchouk EB (2016) Identification of novel microRNA genes in freshwater and marine ecotypes of the three-spined stickleback (Gasterosteus aculeatus). Mol Ecol Resour 16(6):1491–1498
Rengmark AH, Slettan A, Lee WJ, Lie Ø, Lingaas F (2007) Identification and mapping of genes associated with salt tolerance in tilapia. J Fish Biol 71:409–422
Roy S, Leidal AM, Ye J, Ronen SM, Debnath J (2017) Autophagy-dependent shuttling of TBC1D5 controls plasma membrane translocation of GLUT1 and glucose uptake. Mol Cell 67(1):84–95
Sakamoto T, McCormick SD (2006) Prolactin and growth hormone in fish osmoregulation. Gen Comp Endocrinol 147(1):24–30
Salati AP, Baghbanzadeh A, Soltani M, Peyghan R, Riazi G (2011) Effect of different levels of salinity on gill and kidney function in common carp Cyprinus carpio (Pisces: Cyprinidae). Ital J Zool 78(3):298–303
Santoni V, Joëlle V, Pflieger D, Sommerer N, Maurel C (2003) A proteomic study reveals novel insights into the diversity of aquaporin forms expressed in the plasma membrane of plant roots. Bio Chem J 373(1):289–296
Schwer B, Bunkenborg J, Verdin RO, Andersen JS, Verdin E (2006) Reversible lysine acetylation controls the activity of the mitochondrial enzyme acetyl-CoA synthetase 2P. Proc Natl Acad Sci USA 103(27):10224–10229
Shekhar MS, Kiruthika J, Ponniah AG (2013) Identification and expression analysis of differentially expressed genes from shrimp (Penaeus monodon) in response to low salinity stress. Fish Shellfish Immunol 35(6):1957–1968
Shi M, Lin Y, Xu G, Xie L, Hu X, Bao Z, Zhang R (2013) Characterization of the Zhikong scallop (Chlamys farreri) mantle transcriptome and identification of biomineralization-related genes. Mar Biotechnol 15(6):706–715
Starai VJ, Celic I, Cole RN, Boeke JD, Escalante-Semerena JC (2002) Sir2-dependent activation of acetyl-CoA synthetase by deacetylation of active lysine. Science 298(5602):2390–2392
Storey JD, Tibshirani R (2003) Statistical significance for genomewide studies. J Proc Natl Acad Sci 100(16): 9440–9445
Talbot TD, Lawrence JM (2002) The effect of salinity on respiration excretion regeneration and production in Ophiophragmus filograneus (Echinodermata: Ophiuroidea). J Exp Mar Biol Ecol 275(1):1–14
Tamayo D, Corporeau C, Petton B, Quere C, Pernet F (2014) Physiological changes in Pacific oyster Crassostrea gigas exposed to the herpesvirus OsHV-1 μVar. Aquaculture 432:304–310
Tipsmark CK, Kiilerich P, Nilsen TO, Ebbesson LO, Stefansson SO, Madsen SS (2008) Branchial expression patterns of claudin isoforms in Atlantic salmon during seawater acclimation and smoltification. Am J Physiol-RegI 294(5):R1563–R1574
Tipsmark CK, Sørensen KJ, Madsen SS (2010) Aquaporin expression dynamics in osmoregulatory tissues of Atlantic salmon during smoltification and seawater acclimation. J Exp Biol 213(3):368–379
Tournaire-Roux C, Sutka M, Javot H, Gout E, Gerbeau P, Luu DT (2003) Cytosolic pH regulates root water transport during anoxic stress through gating of aquaporins. Nature 425(6956):393
Tse WP, Che CT, Liu K, Lin ZX (2006) Evaluation of the anti-proliferative properties of selected psoriasis-treating Chinese medicines on cultured HaCaT cells. J Ethnopharmacol 108(1):133–141
Vidolin D, Santos-Gouvea IA, Freire CA (2002) Osmotic stability of the coelomic fluids of a sea-cucumber (Holothuria grisea) and a starfish (Asterina stellifera) (Echinodermata) exposed to the air during low tide: a field study. Acta Biol Paranaense 31:113–121
Wang F, Yang H, Gao F, Liu G (2008) Effects of acute temperature or salinity stress on the immune response in sea cucumber Apostichopus japonicas. Comp Biochem Phys A 151(4):491–498
Warner JR, McIntosh KB (2009) How common are extraribosomal functions of ribosomal proteins? Mol Cell 34(1):3–11
Wen M, Shen Y, Shi S, et al. (2012) miREvo: an integrative microRNA evolutionary analysis platform for next-generation sequencing experiments. BMC bioinformatics 13(1):140
Wiedmer T, Zhao J, Li L, Zhou Q, Hevener A, Olefsky JM (2004) Adiposity dyslipidemia and insulin resistance in mice with targeted deletion of phospholipid scramblase 3 (PLSCR3). Proc Natl Acad Sci 101(36):13296–13301
Xu C, Li E, Liu Y, Wang X, Qin JG, Chen L (2017) Comparative proteome analysis of the hepatopancreas from the Pacific white shrimp Litopenaeus vannamei under long-term low salinity stress. J Proteome 162:1–10
Xu Q, Liu Y (2011) Gene expression profiles of the swimming crab Portunus trituberculatus exposed to salinity stress. Mar Biol 158(10):2161
Yan B, Guo JT, Zhao LH, Zhao JL (2012a) MiR-30c: a novel regulator of salt tolerance in tilapia. Biochem Biophys Res Commun 425(2):315–320
Yan B, Wang ZH, Zhao JL (2013) Mechanism of osmoregulatory adaptation in tilapia. Mol Biol Rep 40(2):925–931
Yan B, Zhao LH, Guo JT, Zhao JL (2012b) miR-429 regulation of osmotic stress transcription factor 1 (OSTF1) in tilapia during osmotic stress. Biochem Biophys Res Commun 426(3):294–298
Yan B, Zhao L, Guo J, Zhao J (2012c) miR-206 regulates the growth of the teleost tilapia (Oreochromis niloticus) through the modulation of IGF-1 gene expression. J Exp Biol:079590
Yang Y, Guo Y (2018) Elucidating the molecular mechanisms mediating plant salt-stress responses. New Phytol 217(2):523–539
Yuan X, Yang H, Wang L, Zhou Y, Gabr HR (2010) Effects of salinity on energy budget in pond-cultured sea cucumber Apostichopus japonicus (Selenka) (Echinodermata: Holothuroidea). Aquaculture 306(1–4):348–351
Zacchi FL, de Lima D, Flores-Nunes F, Mattos JJ, Luechmann KH, de Miranda Gomes CHA, Bainy ACD (2017) Transcriptional changes in oysters Crassostrea brasiliana exposed to phenanthrene at different salinities. Aquat Toxicol 183:94–103
Zhang BC, Zhang J, Sun L (2014c) In-depth profiling and analysis of host and viral microRNAs in Japanese flounder (Paralichthys olivaceus) infected with megalocyti virus reveal involvement of microRNAs in host-virus interaction in teleost fish. BMC Genomics 15(1):878
Zhang C, Tong C, Tian F, Zhao K (2017) Integrated mRNA and microRNA transcriptome analyses reveal regulation of thermal acclimation in Gymnocypris przewalskii: a case study in Tibetan Schizothoracine fish. PLoS One 12(10):e0186433
Zhang G, Fang X, Guo X, Li L, Luo R, Xu F (2012) The oyster genome reveals stress adaptation and complexity of shell formation. Nature 490(7418):49
Zhang L, Feng Q, Sun L, Ding K, Huo D, Fang Y (2018) Differential gene expression in the intestine of sea cucumber (Apostichopus japonicus) under low and high salinity conditions. Comp Biochem Phys D 25:34–41
Zhang L, Li L, Zhu Y, Zhang G, Guo X (2014a) Transcriptome analysis reveals a rich gene set related to innate immunity in the Eastern oyster (Crassostrea virginica). Mar Biotechnol 16(1):17–33
Zhang Y, Sun J, Mu H, Li J, Zhang Y, Xu F (2014b) Proteomic basis of stress responses in the gills of the pacific oyster Crassostrea gigas. J Proteome Res 14(1):304–317
Zhao X, Yu H, Kong L, Liu S, Li Q (2016) High throughput sequencing of small RNAs transcriptomes in two Crassostrea oysters identifies microRNAs involved in osmotic stress response. Sci Rep- UK 6:22687
Zhao X, Yu H, Kong L, Li Q (2012) Transcriptomic responses to salinity stress in the Pacific oyster Crassostrea gigas. PLoS One 7(9):e46244
Zhou X, Ren Y, Moore L, Mei M, You Y, Xu P, Wang B, Wang G, Jia Z, Pu P. Zhang W, Kang C (2010) Downregulation of miR-21 inhibits EGFR pathway and suppresses the growth of human glioblastoma cells independent of PTEN status. Lab. Invest. 90:144–155
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The authors are thankful to the National Key Research and Development Program of China (2018YFD0901601), Department of Education of Liaoning Province (L201620) for their financial support.
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Tian, Y., Shang, Y., Guo, R. et al. Salinity stress-induced differentially expressed miRNAs and target genes in sea cucumbers Apostichopus japonicus. Cell Stress and Chaperones 24, 719–733 (2019). https://doi.org/10.1007/s12192-019-00996-y
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DOI: https://doi.org/10.1007/s12192-019-00996-y