Transcriptional events co-regulated by hypoxia and cold stresses in Zebrafish larvae

BMC Genomics

Zongbin Cui¹  Qing Li¹  Xixi Li²  Xiaohui Li²  Guili Song¹  Junjun Yan²  Yong Long¹ 

[1] The Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, PR China;University of the Chinese Academy of Sciences, Beijing, PR China

关键词: Gene expression;    RNA-seq;    Cold stress;    Hypoxia;    Zebrafish;   

Others  :  1203952
DOI  :  10.1186/s12864-015-1560-y

 received in 2014-11-07, accepted in 2015-04-20,  发布年份 2015

【 摘 要 】

Background

Hypoxia and temperature stress are two major adverse environmental conditions often encountered by fishes. The interaction between hypoxia and temperature stresses has been well documented and oxygen is considered to be the limiting factor for the thermal tolerance of fish. Although both high and low temperature stresses can impair the cardiovascular function and the cross-resistance between hypoxia and heat stress has been found, it is not clear whether hypoxia acclimation can protect fish from cold injury.

Results

Pre-acclimation of 96-hpf zebrafish larvae to mild hypoxia (5% O2) significantly improved their resistance to lethal hypoxia (2.5% O2) and increased the survival rate of zebrafish larvae after lethal cold (10°C) exposure. However, pre-acclimation of 96-hpf larvae to cold (18°C) decreased their tolerance to lethal hypoxia although their ability to endure lethal cold increased. RNA-seq analysis identified 132 up-regulated and 41 down-regulated genes upon mild hypoxia exposure. Gene ontology enrichment analyses revealed that genes up-regulated by hypoxia are primarily involved in oxygen transport, oxidation-reduction process, hemoglobin biosynthetic process, erythrocyte development and cellular iron ion homeostasis. Hypoxia-inhibited genes are enriched in inorganic anion transport, sodium ion transport, very long-chain fatty acid biosynthetic process and cytidine deamination. A comparison with the dataset of cold-regulated gene expression identified 23 genes co-induced by hypoxia and cold and these genes are mainly associated with oxidation-reduction process, oxygen transport, hemopoiesis, hemoglobin biosynthetic process and cellular iron ion homeostasis. The alleviation of lipid peroxidation damage by both cold- and hypoxia-acclimation upon lethal cold stress suggests the association of these genes with cold resistance. Furthermore, the alternative promoter of hmbsb gene specifically activated by hypoxia and cold was identified and confirmed.

Conclusions

Acclimation responses to mild hypoxia and cold stress were found in zebrafish larvae and pre-acclimation to hypoxia significantly improved the tolerance of larvae to lethal cold stress. RNA-seq and bioinformatics analyses revealed the biological processes associated with hypoxia acclimation. Transcriptional events co-induced by hypoxia and cold may represent the molecular basis underlying the protection of hypoxia-acclimation against cold injury.

【 授权许可】

   
2015 Long et al.; licensee BioMed Central.

【 图 表 】

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【 参考文献 】

• [1]Wootton RJ. Fish Ecology. Chapman and Hall, USA; 1992.
• [2]Donaldson MR, Cooke SJ, Patterson DA, Macdonald JS. Cold shock and fish. J Fish Biol. 2008; 73(7):1491-530.
• [3]Padilla PA, Roth MB. Oxygen deprivation causes suspended animation in the zebrafish embryo. Proc Natl Acad Sci U S A. 2001; 98(13):7331-5.
• [4]Zuo L, Wagner PD, Roberts WJ, Shia A, Chien MT, Hogan MC. Hypoxia Induced Reactive Oxygen Species Formation during Contractions in Single Skeletal Muscle Fibers. Med Sci Sport Exer. 2013; 45(5):182-2.
• [5]Clanton TL. Hypoxia-induced reactive oxygen species formation in skeletal muscle. J Appl Physiol. 2007; 102(6):2379-88.
• [6]Cervellati F, Cervellati C, Romani A, Cremonini E, Sticozzi C, Belmonte G et al.. Hypoxia induces cell damage via oxidative stress in retinal epithelial cells. Free Radic Res. 2014; 48(3):303-12.
• [7]Nikinmaa M. Oxygen-dependent cellular functions - why fishes and their aquatic environment are a prime choice of study. Comp Biochem Physiol A Integr Physiol. 2002; 133(1):1-16.
• [8]Zhu CD, Wang ZH, Yan BA. Strategies for hypoxia adaptation in fish species: a review. J Comp Physiol B Biochem Syst Environ Physiol. 2013; 183(8):1005-13.
• [9]Breitburg D. Effects of hypoxia, and the balance between hypoxia and enrichment, on coastal fishes and fisheries. Estuaries. 2002; 25(4B):767-81.
• [10]Thomas P, Rahman MS. Biomarkers of hypoxia exposure and reproductive function in Atlantic croaker: A review with some preliminary findings from the northern Gulf of Mexico hypoxic zone. J Exp Mar Biol Ecol. 2009; 381:S38-50.
• [11]Mandic M, Todgham AE, Richards JG. Mechanisms and evolution of hypoxia tolerance in fish. Proc Biol Sci. 2009; 276(1657):735-44.
• [12]Long Y, Song GL, Yan JJ, He XZ, Li Q, Cui ZB. Transcriptomic characterization of cold acclimation in larval zebrafish. BMC Genomics. 2013; 14:612. BioMed Central Full Text
• [13]Rees BB, Sudradjat FA, Love JW. Acclimation to hypoxia increases survival time of zebrafish, Danio rerio, during lethal hypoxia. J Exp Zool. 2001; 289(4):266-72.
• [14]Barrionuevo WR, Fernandes MN, Rocha O. Aerobic and anaerobic metabolism for the zebrafish, Danio rerio, reared under normoxic and hypoxic conditions and exposed to acute hypoxia during development. Braz J Biol. 2010; 70(2):425-34.
• [15]Brady DC, Targett TE, Tuzzolino DM. Behavioral responses of juvenile weakfish (Cynoscion regalis) to diel-cycling hypoxia: swimming speed, angular correlation, expected displacement, and effects of hypoxia acclimation. Can J Fish Aquat Sci. 2009; 66(3):415-24.
• [16]Kind PK, Grigg GC, Booth DT. Physiological responses to prolonged aquatic hypoxia in the Queensland lungfish Neoceratodus forsteri. Respir Physiol Neurobiol. 2002; 132(2):179-90.
• [17]Nilsson GE. Gill remodeling in fish - a new fashion or an ancient secret? J Exp Biol. 2007; 210(14):2403-9.
• [18]Petersen LH, Gamperl AK. Cod (Gadus morhua) Cardiorespiratory Physiology and Hypoxia Tolerance following Acclimation to Low-Oxygen Conditions. Physiol Biochem Zool. 2011; 84(1):18-31.
• [19]Burleson ML, Carlton AL, Silva PE. Cardioventilatory effects of acclimatization to aquatic hypoxia in channel catfish. Respir Physiol Neurobiol. 2002; 131(3):223-32.
• [20]Cameron JS, DeWitt JP, Ngo TT, Yajnik T, Chan S, Chung E et al.. Cardiac K-ATP channel alterations associated with acclimation to hypoxia in goldfish (Carassius auratus L.). Comp Biochem Physiol A Mol Integr Physiol. 2013; 164(4):554-64.
• [21]Vandenthillart G, Smit H. Carbohydrate-Metabolism of Goldfish (Carassius-Auratus L) - Effects of Long-Term Hypoxia-Acclimation on Enzyme Patterns of Red Muscle, White Muscle and Liver. J Comp Physiol. 1984; 154(5):477-86.
• [22]Somero GN, Hochachka PW. Biochemical adaptation to the environment. Am Zool. 1971; 11(1):159-67.
• [23]Johnston PV, Roots BI. Brain Lipid Fatty Acids and Temperature Acclimation. Comp Biochem Physiol. 1964; 11:303-9.
• [24]Gerlach GF, Turay L, Malik KTA, Lida J, Scutt A, Goldspink G. Mechanisms of Temperature-Acclimation in the Carp - a Molecular-Biology Approach. Am J Physiol. 1990; 259(2):R237-44.
• [25]Fader SC, Yu ZM, Spotila JR. Seasonal-Variation in Heat-Shock Proteins (Hsp70) in Stream Fish under Natural Conditions. J Therm Biol. 1994; 19(5):335-41.
• [26]St-Pierre J, Charest PM, Guderley H. Relative contribution of quantitative and qualitative changes in mitochondria to metabolic compensation during seasonal acclimatisation of rainbow trout Oncorhynchus mykiss. J Exp Biol. 1998; 201(21):2961-70.
• [27]Ton C, Stamatiou D, Liew CC. Gene expression profile of zebrafish exposed to hypoxia during development. Physiol Genomics. 2003; 13(2):97-106.
• [28]van der Meer DL, van den Thillart GE, Witte F, de Bakker MA, Besser J, Richardson MK et al.. Gene expression profiling of the long-term adaptive response to hypoxia in the gills of adult zebrafish. Am J Physiol Regul Integr Comp Physiol. 2005; 289(5):R1512-9.
• [29]Martinovic D, Villeneuve DL, Kahl MD, Blake LS, Brodin JD, Ankley GT. Hypoxia alters gene expression in the gonads of zebrafish (Danio rerio). Aquat Toxicol. 2009; 95(4):258-72.
• [30]Marques IJ, Leito JT, Spaink HP, Testerink J, Jaspers RT, Witte F et al.. Transcriptome analysis of the response to chronic constant hypoxia in zebrafish hearts. J Comp Physiol B Biochem Syst Environ physiol. 2008; 178(1):77-92.
• [31]Gracey AY, Troll JV, Somero GN. Hypoxia-induced gene expression profiling in the euryoxic fish Gillichthys mirabilis. Proc Natl Acad Sci U S A. 2001; 98(4):1993-8.
• [32]Zhang ZP, Wells MC, Boswell MG, Beldorth I, Kirk LM, Wang YL et al.. Identification of robust hypoxia biomarker candidates from fin of medaka (Oryzias latipes). Comp Biochem Physiol C. 2012; 155(1):11-7.
• [33]Boswell MG, Wells MC, Kirk LM, Ju ZL, Zhang ZP, Booth RE et al.. Comparison of gene expression responses to hypoxia in viviparous (Xiphophorus) and oviparous (Oryzias) fishes using a medaka microarray. Comp Biochem Physiol C. 2009; 149(2):258-65.
• [34]Long Y, Li L, Li Q, He X, Cui Z. Transcriptomic characterization of temperature stress responses in larval zebrafish. PLoS One. 2012; 7(5):e37209.
• [35]Gracey AY, Fraser EJ, Li W, Fang Y, Taylor RR, Rogers J et al.. Coping with cold: An integrative, multitissue analysis of the transcriptome of a poikilothermic vertebrate. Proc Natl Acad Sci U S A. 2004; 101(48):16970-5.
• [36]Ju Z, Dunham RA, Liu Z. Differential gene expression in the brain of channel catfish (Ictalurus punctatus) in response to cold acclimation. Mol Genet Genomics. 2002; 268(1):87-95.
• [37]Podrabsky JE, Somero GN. Changes in gene expression associated with acclimation to constant temperatures and fluctuating daily temperatures in an annual killifish Austrofundulus limnaeus. J Exp Biol. 2004; 207(13):2237-54.
• [38]Kassahn KS, Crozier RH, Ward AC, Stone G, Caley MJ. From transcriptome to biological function: environmental stress in an ectothermic vertebrate, the coral reef fish Pomacentrus moluccensis. BMC Genomics. 2007; 8:358. BioMed Central Full Text
• [39]Vornanen M, Hassinen M, Koskinen H, Krasnov A. Steady-state effects of temperature acclimation on the transcriptome of the rainbow trout heart. Am J Physiol-Reg I. 2005; 289(4):R1177-84.
• [40]Thorne MAS, Burns G, Fraser KPP, Hillyard G, Clark MS. Transcription profiling of acute temperature stress in the Antarctic plunderfish Harpagifer antarcticus. Mar Genomics. 2010; 3(1):35-44.
• [41]Olsvik PA, Vikesa V, Lie KK, Hevroy EM. Transcriptional responses to temperature and low oxygen stress in Atlantic salmon studied with next-generation sequencing technology. BMC Genomics. 2013; 14:817. BioMed Central Full Text
• [42]Mininni AN, Milan M, Ferraresso S, Petochi T, Di Marco P, Marino G et al.. Liver transcriptome analysis in gilthead sea bream upon exposure to low temperature. BMC Genomics. 2014; 15:765. BioMed Central Full Text
• [43]Kenneth NS, Rocha S. Regulation of gene expression by hypoxia. Biochem J. 2008; 414:19-29.
• [44]McBryan TL, Anttila K, Healy TM, Schulte PM. Responses to Temperature and Hypoxia as Interacting Stressors in Fish: Implications for Adaptation to Environmental Change. Integr Comp Biol. 2013; 53(4):648-59.
• [45]Lannig G, Bock C, Sartoris FJ, Portner HO. Oxygen limitation of thermal tolerance in cod, Gadus morhua L., studied by magnetic resonance imaging and on-line venous oxygen monitoring. Am J Physiol-Reg I. 2004; 287(4):R902-10.
• [46]Mendonca PC, Gamperl AK. The effects of acute changes in temperature and oxygen availability on cardiac performance in winter flounder (Pseudopleuronectes americanus). Comp Biochem Physiol A Mol Integr Physiol. 2010; 155(2):245-52.
• [47]Portner HO. Oxygen- and capacity-limitation of thermal tolerance: a matrix for integrating climate-related stressor effects in marine ecosystems. J Exp Biol. 2010; 213(6):881-93.
• [48]Mark FC, Bock C, Portner HO. Oxygen-limited thermal tolerance in Antarctic fish investigated by MRI and P-31-MRS. Am J Physiol-Reg I. 2002; 283(5):R1254-62.
• [49]Burleson ML, Silva PE. Cross tolerance to environmental stressors: Effects of hypoxic acclimation on cardiovascular responses of channel catfish (Ictalurus punctatus) to a thermal challenge. J Therm Biol. 2011; 36(4):250-4.
• [50]Heise K, Estevez MS, Puntarulo S, Galleano M, Nikinmaa M, Portner HO et al.. Effects of seasonal and latitudinal cold on oxidative stress parameters and activation of hypoxia inducible factor (HIF-1) in zoarcid fish. J Comp Physiol B Biochem Syst Environ Physiol. 2007; 177(7):765-77.
• [51]Rissanen E, Tranberg HK, Sollid J, Nilsson GE, Nikinmaa M. Temperature regulates hypoxia-inducible factor-1 (HIF-1) in a poikilothermic vertebrate, crucian carp (Carassius carassius). J Exp Biol. 2006; 209(6):994-1003.
• [52]Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 2009; 10(1):57-63.
• [53]Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ et al.. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010; 28(5):511-5.
• [54]Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, Speleman F: Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol. 2002;3(7):research0034.1–0034.11.
• [55]Andersen CL, Jensen JL, Orntoft TF. Normalization of real-time quantitative reverse transcription-PCR data: A model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets. Cancer Res. 2004; 64(15):5245-50.
• [56]Altland PD, Highman B, Dieter MP. Reduced Hypoxic Tolerance of Cold-Acclimated Rats - Serum Enzyme and Tissue Changes. Am J Physiol. 1972; 222(6):1441-5.
• [57]To-Figueras J, Ducamp S, Clayton J, Badenas C, Delaby C, Ged C et al.. ALAS2 acts as a modifier gene in patients with congenital erythropoietic porphyria. Blood. 2011; 118(6):1443-51.
• [58]Tacchini L, Bianchi L, Bernelli-Zazzera A, Cairo G. Transferrin receptor induction by hypoxia - HIF-1-mediated transcriptional activation and cell-specific post-transcriptional regulation. J Biol Chem. 1999; 274(34):24142-6.
• [59]Bruce LJ, Pan RJ, Cope DL, Uchikawa M, Gunn RB, Cherry RJ et al.. Altered structure and anion transport properties of band 3 (AE1, SLC4A1) in human red cells lacking glycophorin A. J Biol Chem. 2004; 279(4):2414-20.
• [60]Ferreira R, Ohneda K, Yamamoto M, Philipsen S. GATA1 function, a paradigm for transcription factors in hematopoiesis. Mol Cell Biol. 2005; 25(4):1215-27.
• [61]Xia XB, Kung AL: Preferential binding of HIF-1 to transcriptionally active loci determines cell-type specific response to hypoxia. Genome Biol. 2009;10(10):R113.
• [62]del Peso L, Castellanos MC, Temes E, Martin-Puig S, Cuevas Y, Olmos G et al.. The von Hippel Lindau/hypoxia-inducible factor (HIF) pathway regulates the transcription of the HIF-proline hydroxylase genes in response to low oxygen. J Biol Chem. 2003; 278(49):48690-5.
• [63]Marxsen JH, Stengel P, Doege K, Heikkinen P, Jokilehto T, Wagner T et al.. Hypoxia-inducible factor-1 (HIF-1) promotes its degradation by induction of HIF-alpha-prolyl-4-hydroxylases. Biochem J. 2004; 381:761-7.
• [64]Kaelin WG, Ratcliffe PJ. Oxygen sensing by metazoans: The central role of the HIF hydroxylase pathway. Mol Cell. 2008; 30(4):393-402.
• [65]Joanisse DR, Storey KB. Oxidative stress and antioxidants in overwintering larvae of cold-hardy goldenrod gall insects. J Exp Biol. 1996; 199(7):1483-91.
• [66]Kaushik S, Kaur J. Chronic cold exposure affects the antioxidant defense system in various rat tissues. Clin Chim Acta. 2003; 333(1):69-77.
• [67]Chao DM, He XZ, Yang YL, Balboni G, Salvadori S, Kim DH et al.. Hydrogen Sulfide Induced Disruption of Na + Homeostasis in the Cortex. Toxicol Sci. 2012; 128(1):198-208.
• [68]Chepelev NL, Willmore WG. Regulation of iron pathways in response to hypoxia. Free Radic Biol Med. 2011; 50(6):645-66.
• [69]Ohyama Y, Meaney S, Heverin M, Ekstrom L, Brafman A, Shafir M et al.. Studies on the transcriptional regulation of cholesterol 24-hydroxylase (CYP46A1) - Marked insensitivity toward different regulatory axes. J Biol Chem. 2006; 281(7):3810-20.
• [70]Cooper RA. Influence of Increased Membrane Cholesterol on Membrane Fluidity and Cell-Function in Human Red Blood-Cells. J Supramol Struct. 1978; 8(4):413-30.
• [71]Cossins AR, Williams DR, Foulkes NS, Berenbrink M, Kipar A. Diverse cell-specific expression of myoglobin isoforms in brain, kidney, gill and liver of the hypoxia-tolerant carp and zebrafish. J Exp Biol. 2009; 212(5):627-38.
• [72]Wittenberg JB, Wittenberg BA. Myoglobin function reassessed. J Exp Biol. 2003; 206(12):2011-20.
• [73]Ayoubi TAY, VanDeVen WJM. Regulation of gene expression by alternative promoters. Faseb J. 1996; 10(4):453-60.
• [74]Kudoh T, Tsang M, Hukriede NA, Chen XF, Dedekian M, Clarke CJ et al.. A gene expression screen in zebrafish embryogenesis. Genome Res. 2001; 11(12):1979-87.
• [75]Chretien S, Dubart A, Beaupain D, Raich N, Grandchamp B, Rosa J et al.. Alternative Transcription and Splicing of the Human Porphobilinogen Deaminase Gene Result Either in Tissue-Specific or in Housekeeping Expression. Proc Natl Acad Sci U S A. 1988; 85(1):6-10.
• [76]Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N et al.. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009; 25(16):2078-9.
• [77]Thorvaldsdottir H, Robinson JT, Mesirov JP: Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Briefings in bioinformatics. 2013;14(2):178–92.
• [78]Maere S, Heymans K, Kuiper M. BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks. Bioinformatics. 2005; 21(16):3448-9.
• [79]Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D et al.. Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res. 2003; 13(11):2498-504.
• [80]Foldager CB, Munir S, Ulrik-Vinther M, Soballe K, Bunger C, Lind M. Validation of suitable house keeping genes for hypoxia-cultured human chondrocytes. BMC Mol Biol. 2009; 10:94. BioMed Central Full Text
• [81]Hellemans J, Mortier G, De Paepe A, Speleman F, Vandesompele J. qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data. Genome Biol. 2007; 8(2):R19. BioMed Central Full Text