Abstract
This paper aims to validate reference genes for gene expression studies between light and dark conditions in the scleractinian coral Stylophora pistillata for future gene expression studies of the “light-enhanced calcification” phenomenon. For this purpose, we cloned, sequenced, and characterized a candidate reference gene, the 36B4 gene from the coral S. pistillata, and validated 36B4 and β-actin as reference genes. To illustrate the future applications of these reference genes, we tested the dark and light expression of two photosynthetic genes (Rubisco and D1 protein of the photosystem II) and two genes encoding proteins involved in calcium transport for coral calcification (a calcium ATPase and a calcium channel). Results show that both photosynthetic genes are enhanced during the light when standardized against 36B4 and β-actin, whereas the two genes encoding proteins involved in calcium transport are not differentially expressed between light and dark conditions. The characterization of a coral 36B4 and the establishment of such valid reference genes will be useful for future gene expression studies between diverse conditions (aposymbiotic/symbiotic, stress/control, light/dark conditions) in scleractinian corals.
Similar content being viewed by others
Abbreviations
- 36B4 = RPLP0:
-
acidic ribosomal phosphoprotein P0
- STP36B4:
-
acidic ribosomal phosphoprotein P0 of the scleractinian coral Stylophora pistillata
- C T :
-
threshold cycle
References
Abascal F, Zardoya R, Posada D (2005) ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21:2104–2105
Akamine R, Yamamoto T, Watanabe M, Yamazaki N, Kataoka M, Ishikawa M, Ooie T, Baba Y, Shinohara Y (2007) Usefulness of the 5¢ region of the cDNA encoding acidic ribosomal phosphoprotein P0 conserved among rats, mice, and humans as a standard probe for gene expression analysis in different tissues and animal species. J Biochem Biophys Methods 70:481–486
Biederman J, Yee J, Cortes P (2004) Validation of internal control genes for gene expression analysis in diabetic glomerulosclerosis. Kidney Int 66:2308–2314
Blankenship KA, Dawson CB, Aronoff GR, Dean WL (2000) Tyrosine phosphorylation of human platelet plasma membrane Ca2+-ATPase in hypertension. Hypertension 35:103–107
Bridge D, Cunnintham CW, Desalle R, Buss LW (1995) Class-level relationships in the phylum Cnidaria: molecular and morphological evidence. Mol Biol Evol 12:679–689
Chomczynski P, Sacchi N (1987) Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem 162:156–159
Ciccarelli F, Doerks T, Von Mering C, Creevey C, Snell B, Bork P (2006) Toward automatic reconstruction of a highly resolved tree of life. Science 311:1283–1287
Deboer M, Krupp DA, Weis VM (2006) Two atypical carbonic anhydrase homologs from the planula larva of the scleractinian coral Fungia scutaria. Biol Bull 211:18–30
Delsuc F, Brinkmann H, Philippe H (2005) Phylogenomics and the reconstruction of the tree of life. Nature 6:361–365
Dent AL, Shaffer AL, Yu X, Allman D, Staudt LM (1997) Control of inflammation, cytokine expression, and germinal center formation by BCL-6. Science 276:589–592
Dunn SR, Phillips WS, Green DR, Weis VM (2007) Knockdown of actin and caspase gene expression by RNA interference in the symbiotic anemone Aiptasia pallida. Biol Bull 212:250–258
Edge SE, Morgan MB, Gleason DF, Snell TW (2005) Development of a coral cDNA array to examine gene expression profiles in Montastraea faveolata exposed to environmental stress. Mar Pollut Bull 51:507–523
Ernst D, Apfelbock A, Bergmann A, Weyrauch C (1990) Rhythmic regulation of the light-harvesting chlorophyll a/b protein and the small subunit of ribulose-1,5-bisphosphate carboxylase mRNA in rye seedlings. Photochem Photobiol 52:29–33
Gagou M, Ballesta JP, Kouyanou S (2000) Cloning and characterization of the ribosomal protein CcP0 of the medfly Ceratitis capitata. Insect Mol Biol 9:47–55
Guarinos E, Remacha M, Ballesta JP (2001) Asymmetric interactions between the acidic P1 and P2 proteins in the Saccharomyces cerevisiae ribosomal stalk. J Biol Chem 276:32474–32479
Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52:696–704
Hayward DC, Samuel G, Pontynen PC, Catmull J, Saint R, Miller DJ, Ball EE (2002) Localized expression of a dpp/BMP2/4 ortholog in a coral embryo. PNAS 99:8116–8111
Hell JW, Yokoyama CT, Breeze LJ, Chavkin C, Catterall WA (1995) Phosphorylation of presynaptic and postsynaptic calcium channels by cAMP-dependent protein kinase in hippocampal neurons. EMBO J 14:3036–3044
Hsiao LL, Dangond F, Yoshida T, Hong R, Jensen RV, Misra J, Dillon W, Lee KF, Clark KE, Haverty P, Weng Z, Mutter GL, Frosch MP, Macdonald ME, Milford EL, Crum CP, Bueno R, Pratt RE, Mahadevappa M, Warrington JA, Stephanopoulos G, Stephanopoulos G, Gullans SR (2001) A compendium of gene expression in normal human tissues. Physiol Genomics 7:97–104
Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17:754–755
Ip YK, Lim ALL, Lim RWL (1991) Some properties of calcium-activated adenosine triphosphatase from the hermatypic coral Galaxea fascicularis. Mar Biol 111:191–197
Ishii K, Washio T, Uechi T, Yoshihama M, Kenmochi N, Tomita M (2006) Characteristics and clustering of human ribosomal protein genes. BMC Genomics 7:37
Jayachandran G, Fallon AM (2003) Ribosomal protein P0 from Aedes albopictus mosquito cells: cDNA cloning and analysis of expression. Genetica 119:1–10
Jorgensen SM, Kleveland EJ, Grimholt U, Gjoen T (2006) Validation of reference genes for real-time polymerase chain reaction studies in Atlantic salmon. Mar Biotechnol (NY) 8:398–408
Kamp TJ, Mitas M, Fields KL, Asoh S, Chin HM, Marban E, Nirenberg M (1995) Transcriptional regulation of the neuronal L-type calcium channel a1D subunit gene. Cell Mol Neurobiol 15:307–326
Karako-Lampert S, Hershkovits G, Stambler N, Simon-Blecher N, Achituv Y, Dubinsky Z, Katcoff DJ (2006) Differential gene expression in Symbiodinium microadriaticum clade B following stress. Mar Biotechnol (NY) 8:268–274
Karge WH, Schaefer EJ, Ordovas JM (1998) Quantification of mRNA by polymerase chain reaction (PCR) using an internal standard and a nonradioactive detection method. Methods Mol Biol 110:43–61
Kip SN, Strehler EE (2004) Vitamin D3 upregulates plasma membrane Ca2+-ATPase expression and potentiates apico-basal Ca2+ flux in MDCK cells. Am J Physiol Renal Physiol 286:F363–F369
Kortschak RD, Samuel G, Saint R, Miller DJ (2003) EST analysis of the Cnidarian Acropora millemora reveals extensive gene loss and rapid sequence divergence in the model invertebrates. Curr Biol 13:2190–2195
Kuo TH, Wang KK, Carlock L, Diglio C, Tsang W (1991) Phorbol ester induces both gene expression and phosphorylation of the plasma membrane Ca2+ pump. J Biol Chem 266:2520–2525
Kuo TH, Liu BF, Diglio C, Tsang W (1993) Regulation of the plasma membrane calcium pump gene expression by two signal transduction pathways. Arch Biochem Biophys 305:428–433
Laborda J (1991) 36B4 cDNA used as an estradiol-independent mRNA control is the cDNA for human acidic ribosomal phosphoprotein PO. Nucleic Acids Res 19:3998
Levy O, Appelbaum L, Leggat W, Gothlif Y, Hayward DC, Miller DJ, Hoegh-Guldberg O (2007) Light-responsive cryptochromes from a simple multicellular animal, the coral Acropora millepora. Science 318:467–470
Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real time quantitative PCR and the 2-DDCT method. Methods 25:402–408
Mamic TM, Holman NA, Roberts-Thomson SJ, Monteith GR (2000) PMCA1 mRNA expression in rat aortic myocytes: a real-time RT-PCR study. Biochem Biophys Res Commun 276:1024–1027
Marshall AT (1996) Calcification in hermatypic and ahermatypic corals. Science 271:637–639
Mitchelmore CL, Schwarz JA, Weis VM (2002) Development of symbiosis-specific genes as biomarkers for the early detection of Cnidarian–algal symbiosis breakdown. Mar Environ Res 54:345–349
Morgan MB, Edge SE, Snell TW (2005) Profiling differential gene expression of corals along a transect of waters adjacent to the Bermuda municipal dump. Mar Pollut Bull 51:524–533
Moya A, Tambutté S, Tambutté E, Zoccola D, Caminiti N, Allemand D (2006) Study of calcification during a daily cycle of the coral Stylophora pistillata: implications for “light-enhanced calcification”. J Exp Biol 209:3413–3419
Muscatine L, Falkowski PG, Dubinski Z, Cook PA, Mc Closkey LR (1989) The effects of external nutrient sources on the population dynamics of zooxanthellae in a reef coral. Proc R Soc Lond B236:311–324
Nassoury N, Fritz L, Morse D (2001) Circadian changes in ribulose-1,5-bisphosphate carboxylase/oxygenase distribution inside individual chloroplasts can account for the rhythm in dinoflagellate carbon fixation. Plant Cell 13:923–934
Plantivaux A, Furla P, Zoccola D, Garello G, Forcioli D, Richier S, Merle PL, Tambutte E, Tambutte S, Allemand D (2004) Molecular characterization of two CuZn-superoxide dismutases in a sea anemone. Free Radic Biol Med 37:1170–1181
Pucciarelli S, Marziale F, Di Giuseppe G, Barchetta S, Miceli C (2005) Ribosomal cold-adaptation: characterization of the genes encoding the acidic ribosomal P0 and P2 proteins from the Antarctic ciliate Euplotes focardii. Gene 360:103–110
Rodriguez-Lanetty M, Phillips WS, Weis VM (2006) Transcriptome analysis of a Cnidarian–dinoflagellate mutualism reveals complex modulation of host gene expression. BioMed Central 7:23
Rodriguez-Lanetty M, Phillips WS, Dove S, Hoegh-Guldberg O, Weis VM (2008) Analytical approach for selecting normalizing genes from a cDNA microarray platform to be used in q-RT-PCR assays: a Cnidarian case study. J Biochem Biophys Methods (in press) DOI 10.1016/j.jbbm.2007.08.005
Roge R, Thorsen J, Torring C, Ozbay A, Moller BK, Carstens J (2007) Commonly used reference genes are actively regulated in in vitro stimulated lymphocytes. Scand J Immunol 65:202–209
Sanchez S, Andersen AC, Hourdez S, Lallier FH (2007) Identification, sequencing, and localization of a new carbonic anhydrase transcript from the hydrothermal vent tubeworm Riftia pachyptila. FEBS J 274:5311–5324
Schaffer R, Landgraf J, Accerbi M, Simon V, Larson M, Wisman E (2001) Microarray analysis of diurnal and circadian-regulated genes in Arabidopsis. Plant Cell 13:113–123
Schroth W, Ender A, Schierwater B (2005) Molecular biomarkers and adaptation to environmental stress in moon jelly (Aurelia spp.). Mar Biotechnol (NY) 7:449–461
Shirley BW, Ham DP, Senecoff JF, Berry-Lowe SL, Zurfluh LL, Shah DM, Meagher RB (1990) Comparison of the expression of two highly homologous members of the soybean ribulose-1,5-bisphosphate carboxylase small subunit gene family. Plant Mol Biol 14:909–925
Simkiss K (1984) The karyotic mineralization window (KMW). Amer Zool 24:847–856
Spring J, Yanze N, Middel AM, Stierwald M, Gröger H, Schmid V (2000) The mesoderm specification factor twist in the life cycle of jellyfish. Dev Biol 228:363–375
Sturzenbaum SR, Kille P (2001) Control genes in quantitative molecular biological techniques: the variability of invariance. Comp Biochem Physiol 130B:281–289
Takeuchi T, Endo K (2006) Biphasic and dually coordinated expression of the genes encoding major shell matrix proteins in the pearl oyster Pinctada fucata. Mar Biotechnol 8:52–61
Tambutté E, Allemand D, Mueller E, Jaubert J (1996) A compartmental approach to the mechanism of calcification in hermatypic corals. J Exp Biol 199:1029–1041
Titlyanov EA, Titlyanova TV, Leletkin VA, Tsukahara J, Van Woesik R, Yamazato K (1996) Degradation of zooxanthellae and regulation of their density in hermatypic corals. Mar Ecol Prog Ser 139:167–178
Uchiumi T, Kikuchi M, Terao K, Iwasaki K, Ogata K (1986) Cross-linking of elongation factor 2 to rat-liver ribosomal proteins by 2-iminothiolane. Eur J Biochem 156:37–48
Van Dolah FM, Lidie KB, Morey JS, Brunelle SA, Ryan JC, Monroe EA, Haynes BL (2007) Microarray analysis of diurnal- and circadian-regulated genes in the Florida red-tide dinoflagellate Karenia brevis (Dinophyceae). J Phycol 43:741–752
Wang Y, Jenson L, Hojrup P, Morse D (2005) Synthesis and degradation of dinoflagellate encoded psbA proteins are light-regulated, not circadian regulated. Proc Natl Acad Sci U S A 102:2844–2849
Yuyama I, Hayakawa H, Endo H, Iwao K, Takeyama H, Maruyama T, Watanabe T (2005) Identification of symbiotically expressed coral mRNAs using a model infection system. Biochem Biophys Res Commun 336:793–798
Zoccola D, Tambutté É, Sénegas-Balas F, Michiels J-F, Failla J-P, Jaubert J, Allemand D (1999) Cloning of a calcium channel a1 subunit from the reef-building coral, Stylophora pistillata. Gene 227:157–167
Zoccola D, Tambutté E, Kulhanek E, Puverel S, Scimeca JC, Allemand D, Tambutté S (2004) Molecular cloning and localization of a PMCA P-type calcium ATPase from the coral Stylophora pistillata. Biochim Biophys Acta 1663:117–126
Acknowledgments
We thank the three referees for their helpful comments on this manuscript. We are grateful to Dr. Didier Forcioli for his help in phylogenetic analyses and to Dominique Desgré for coral maintenance. Aurélie Moya was supported by a fellowship from the Scientific Center of Monaco. This study was conducted as part of the Centre Scientifique de Monaco Research Program, supported by the Government of the Principality of Monaco.
Author information
Authors and Affiliations
Corresponding author
Additional information
Nucleotide sequence of the coral 36B4 gene cloned in this study is available in the Genbank database under the accession number EU069460.
Rights and permissions
About this article
Cite this article
Moya, A., Tambutté, S., Béranger, G. et al. Cloning and Use of a Coral 36B4 Gene to Study the Differential Expression of Coral Genes Between Light and Dark Conditions. Mar Biotechnol 10, 653–663 (2008). https://doi.org/10.1007/s10126-008-9101-1
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10126-008-9101-1