Transcriptomic characterization of temperature stress responses in larval zebrafish

PLoS ONE

Volumn 7, Issue 5, 2012, Pages

  Long, Yong ^a   Li, Linchun ^b   Li, Qing ^a   He, Xiaozhen ^a   Cui, Zongbin ^a  

^a INSTITUTE OF HYDROBIOLOGY   (China)

^b Xiamen Ocean Vocational College   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ADIPOCYTOKINE; ARGININE; MAMMALIAN TARGET OF RAPAMYCIN; PROLINE; PROTEIN P53;

AMINO ACID METABOLISM; ANIMAL TISSUE; ARTICLE; BIOINFORMATICS; CHROMATIN ASSEMBLY AND DISASSEMBLY; CIRCADIAN RHYTHM; COLD EXPOSURE; COLD STRESS; CONTROLLED STUDY; EMBRYO; GENE EXPRESSION; GENETIC TRANSCRIPTION; HEAT STRESS; LARVAL DEVELOPMENT; METAL METABOLISM; MICROARRAY ANALYSIS; NONHUMAN; NUCLEOSOME; PROTEIN FOLDING; PROTEIN TRANSPORT; RNA PROCESSING; SIGNAL TRANSDUCTION; TEMPERATURE STRESS; THERMAL EXPOSURE; TRANSCRIPTION REGULATION; TRANSCRIPTOMICS; UPREGULATION; ZEBRA FISH; ADAPTATION; ANIMAL; ANIMAL EMBRYO; BODY COMPOSITION; COLD; CYTOLOGY; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENETICS; GROWTH, DEVELOPMENT AND AGING; HEAT; LARVA; METABOLISM; OLIGONUCLEOTIDE PROBE; PHYSIOLOGICAL STRESS; PHYSIOLOGY; PRENATAL DEVELOPMENT; TEMPERATURE;

DANIO RERIO;

ADAPTATION, PHYSIOLOGICAL; ANIMALS; BODY COMPOSITION; COLD TEMPERATURE; EMBRYO, NONMAMMALIAN; GENE EXPRESSION PROFILING; HOT TEMPERATURE; LARVA; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OLIGONUCLEOTIDE PROBES; SIGNAL TRANSDUCTION; STRESS, PHYSIOLOGICAL; TEMPERATURE; ZEBRAFISH;

EID: 84861617075     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0037209     Document Type: Article

References (63)

1. Somero GN, (1995) Proteins and temperature. Annu Rev Physiol 57: 43-68.
2. Pan J, Tristram-Nagle S, Kucerka N, Nagle JF, (2008) Temperature dependence of structure, bending rigidity, and bilayer interactions of dioleoylphosphatidylcholine bilayers. Biophys J 94: 117-124.
3. Simon SA, Advani S, Mcintosh TJ, (1995) Temperature-Dependence of the Repulsive Pressure between Phosphatidylcholine Bilayers. Biophys J 69: 1473-1483.
4. Ueda MJ, Ito T, Okada TS, Ohnishi SI, (1976) A correlation between membrane fluidity and the critical temperature for cell adhesion. J Cell Biol 71: 670-674.
5. Johnston IA, Bennett AF, (1996) Animals and temperature: phenotypic and evolutionary adaptation. New York: Cambridge University Press. xvi: 419.
6. Donaldson MR, Cooke SJ, Patterson DA, Macdonald JS, (2008) Cold shock and fish. J Fish Biol 73: 1491-1530.
7. Beitinger TL, Bennett WA, McCauley RW, (2000) Temperature tolerances of North American freshwater fishes exposed to dynamic changes in temperature. Environ Biol Fishes 58: 237-275.
8. Cossins AR, Crawford DL, (2005) Opinion- Fish as models for environmental genomics. Nat Rev Genet 6: 324-333.
9. Ju Z, Dunham RA, Liu Z, (2002) Differential gene expression in the brain of channel catfish (Ictalurus punctatus) in response to cold acclimation. Mol Genet Genomics 268: 87-95.
10. Podrabsky JE, Somero GN, (2004) Changes in gene expression associated with acclimation to constant temperatures and fluctuating daily temperatures in an annual killifish Austrofundulus limnaeus. J Exp Biol 207: 2237-2254.
11. Somero GN, Hochachka PW, (1971) Biochemical adaptation to the environment. Am Zool 11: 159-167.
12. Hochachka PW, Lewis JK, (1970) Enzyme variants in thermal acclimation. Trout liver citrate synthases. J Biol Chem 245: 6567-6573.
13. Johnston PV, Roots BI, (1964) Brain Lipid Fatty Acids and Temperature Acclimation. Comp Biochem Physiol 11: 303-309.
14. Gerlach GF, Turay L, Malik KT, Lida J, Scutt A, et al. (1990) Mechanisms of temperature acclimation in the carp: a molecular biology approach. Am J Physiol 259: R237-244.
15. Fader SC, Yu ZM, Spotila JR, (1994) Seasonal-Variation in Heat-Shock Proteins (Hsp70) in Stream Fish under Natural Conditions. J Therm Biol 19: 335-341.
16. diIorio PJ, Holsinger K, Schultz RJ, Hightower LE, (1996) Quantitative evidence that both Hsc70 and Hsp70 contribute to thermal adaptation in hybrids of the livebearing fishes Poeciliopsis. Cell Stress Chaperones 1: 139-147.
17. St-Pierre J, Charest PM, Guderley H, (1998) Relative contribution of quantitative and qualitative changes in mitochondria to metabolic compensation during seasonal acclimatisation of rainbow trout Oncorhynchus mykiss. J Exp Biol 201: 2961-2970.
18. Driedzic WR, Bailey JR, Sephton DH, (1996) Cardiac adaptations to low temperature non-polar teleost fish. J Exp Zool 275: 186-195.
19. Devries AL, (1971) Glycoproteins as Biological Antifreeze Agents in Antarctic Fishes. Science 172: 1152-1155.
20. Goldspink G, (1995) Adaptation of Fish to Different Environmental-Temperature by Qualitative and Quantitative Changes in Gene-Expression. J Therm Biol 20: 167-174.
21. Gracey AY, Fraser EJ, Li W, Fang Y, Taylor RR, et al. (2004) Coping with cold: An integrative, multitissue analysis of the transcriptome of a poikilothermic vertebrate. Proc Natl Acad Sci U S A 101: 16970-16975.
22. Vergauwen L, Benoot D, Blust R, Knapen D, (2010) Long-term warm or cold acclimation elicits a specific transcriptional response and affects energy metabolism in zebrafish. Comp Biochem Physiol A Mol Integr Physiol 157: 149-157.
23. Chou MY, Hsiao CD, Chen SC, Chen IW, Liu ST, et al. (2008) Effects of hypothermia on gene expression in zebrafish gills: upregulation in differentiation and function of ionocytes as compensatory responses. J Exp Biol 211: 3077-3084.
24. Kassahn KS, Crozier RH, Ward AC, Stone G, Caley MJ, (2007) From transcriptome to biological function: environmental stress in an ectothermic vertebrate, the coral reef fish Pomacentrus moluccensis. BMC Genomics 8: 358.
25. Kassahn KS, Caley MJ, Ward AC, Connolly AR, Stone G, et al. (2007) Heterologous microarray experiments used to identify the early gene response to heat stress in a coral reef fish. Mol Ecol 16: 1749-1763.
26. Logan CA, Somero GN, (2011) Effects of thermal acclimation on transcriptional responses to acute heat stress in the eurythermal fish Gillichthys mirabilis (Cooper). Am J Physiol Regul Integr Comp Physiol 300: R1373-R1383.
27. Buckley BA, Gracey AY, Somero GN, (2006) The cellular response to heat stress in the goby Gillichthys mirabilis: a cDNA microarray and protein-level analysis. J Exp Biol 209: 2660-2677.
28. Vornanen M, Hassinen M, Koskinen H, Krasnov A, (2005) Steady-state effects of temperature acclimation on the transcriptome of the rainbow trout heart. Am J Physiol Regul Integr Comp Physiol 289: R1177-1184.
29. Green BS, Fisher R, (2004) Temperature influences swimming speed, growth and larval duration in coral reef fish larvae. J Exp Mar Biol Ecol 299: 115-132.
30. Beitinger TL, Cortemeglia C, (2005) Temperature tolerances of wild-type and red transgenic zebra danios. Trans Am Fish Soc 134: 1431-1437.
31. Schaefer J, Ryan A, (2006) Developmental plasticity in the thermal tolerance of zebrafish Danio rerio. J Fish Biol 69: 722-734.
32. Mukhi S, Patino R, (2007) Effects of prolonged exposure to perchlorate on thyroid and reproductive function in zebrafish. Toxicol Sci 96: 246-254.
33. Andersen CL, Jensen JL, Orntoft TF, (2004) 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 64: 5245-5250.
34. Plaisier SB, Taschereau R, Wong JA, Graeber TG, (2010) Rank-rank hypergeometric overlap: identification of statistically significant overlap between gene-expression signatures. Nucleic Acids Res 38.
35. Trezise AE, Collin SP, (2005) Opsins: evolution in waiting. Curr Biol 15: R794-796.
36. Young JC, Moarefi I, Hartl FU, (2001) Hsp90: a specialized but essential protein-folding tool. J Cell Biol 154: 267-273.
37. Ojha J, Masilamoni G, Dunlap D, Udoff RA, Cashikar AG, (2011) Sequestration of toxic oligomers by HspB1 as a cytoprotective mechanism. Mol Cell Biol 31: 3146-3157.
38. Weidenhammer EM, Singh M, Ruiz-Noriega M, Woolford JL Jr, (1996) The PRP31 gene encodes a novel protein required for pre-mRNA splicing in Saccharomyces cerevisiae. Nucleic Acids Res 24: 1164-1170.
39. Parichy DM, Elizondo MR, Mills MG, Gordon TN, Engeszer RE, (2009) Normal table of postembryonic zebrafish development: staging by externally visible anatomy of the living fish. Dev Dyn 238: 2975-3015.
40. Kimmel CB, Ballard WW, Kimmel SR, Ullmann B, Schilling TF, (1995) Stages of embryonic development of the zebrafish. Dev Dyn 203: 253-310.
41. Thomashow MF, (2010) Molecular basis of plant cold acclimation: insights gained from studying the CBF cold response pathway. Plant Physiol 154: 571-577.
42. Aranda A, Pascual A, (2001) Nuclear hormone receptors and gene expression. Physiol Rev 81: 1269-1304.
43. Lazar MA, Yin L, Wu N, Curtin JC, Qatanani M, et al. (2007) Rev-erb alpha, a heme sensor that coordinates metabolic and circadian pathways. Science 318: 1786-1789.
44. Burris TP, (2008) Nuclear hormone receptors for heme: REV-ERB alpha and REV-ERB beta are ligand-regulated components of the mammalian clock. Mol Endocrinol 22: 1509-1520.
45. Ryabinin AE, Bachtell RK, Tsivkovskaia NO, (2003) Identification of temperature-sensitive neural circuits in mice using c-Fos expression mapping. Brain Res 960: 157-164.
46. McKitrick DJ, (2000) Expression of fos in the hypothalamus of rats exposed to warm and cold temperatures. Brain Res Bull 53: 307-315.
47. Joyce MP, Barr GA, (1992) The appearance of Fos protein-like immunoreactivity in the hypothalamus of developing rats in response to cold ambient temperatures. Neuroscience 49: 163-173.
48. Thornhill JA, Halvorson I, (1994) Electrical stimulation of the posterior and ventromedial hypothalamic nuclei causes specific activation of shivering and nonshivering thermogenesis. Can J Physiol Pharmacol 72: 89-96.
49. Long Y, Li Q, Zhong S, Wang YH, Cui ZB, (2011) Molecular characterization and functions of zebrafish ABCC2 in cellular efflux of heavy metals. Comp Biochem Physiol Part C Toxicol Pharmcol 153: 381-391.
50. Schilling TF, Piotrowski T, Grandel H, Brand M, Heisenberg CP, et al. (1996) Jaw and branchial arch mutants in zebrafish I: branchial arches. Development 123: 329-344.
51. Cheng YS, Zheng Y, VanderGheynst JS, (2011) Rapid Quantitative Analysis of Lipids Using a Colorimetric Method in a Microplate Format. Lipids 46: 95-103.
52. Templeton M, (1961) Microdetermination of Glycogen with Anthrone Reagent. J Histochem Cytochem 9: 670-672.
53. Fang H, (2009) The FDA Genomics Tool- ArrayTrack. Molecular & Cellular Toxicology 5: 40-40.
54. Saeed AI, Bhagabati NK, Braisted JC, Liang W, Sharov V, et al. (2006) TM4 microarray software suite. Methods Enzymol 411: 134-193.
55. Reimand J, Arak T, Vilo J, (2011) g: Profiler-a web server for functional interpretation of gene lists. Nucleic Acids Res 39: W307-W315.
56. Xu J, Kelly R, Fang H, Tong W, (2010) ArrayTrack: a free FDA bioinformatics tool to support emerging biomedical research-an update. Hum Genomics 4: 428-434.
57. Wang XJ, Zheng Q, (2008) GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis. Nucleic Acids Res 36: W358-W363.
58. Bindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, et al. (2009) ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics 25: 1091-1093.
59. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, et al. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13: 2498-2504.
60. Perez-Llamas C, Lopez-Bigas N, (2011) Gitools: Analysis and Visualisation of Genomic Data Using Interactive Heat-Maps. PLoS One 6.
61. Saldanha AJ, (2004) Java Treeview-extensible visualization of microarray data. Bioinformatics 20: 3246-3248.
62. Muller PY, Janovjak H, Miserez AR, Dobbie Z, (2002) Processing of gene expression data generated by quantitative real-time RT-PCR. BioTechniques 32: 1372-1374, 1376, 1378-1379.
63. Dennis G Jr, Sherman BT, Hosack DA, Yang J, Gao W, et al. (2003) DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol 4: P3.