Abstract
Calmodulin (CaM), belonging to the tropinin C (TnC) superfamily, is one of the calcium-binding proteins that are highly conserved in their protein and gene structure. Based on the structure comparison among published vertebrate and invertebrate CaM, it is proposed that the ancestral form of eumetazoan CaM genes should have five exons and four introns (four-intron hypothesis). In this study, we determined the gene structure of CaM in the coral Acropora muricata, an anthozoan cnidarian representing the basal position in animal evolution. A CaM clone was isolated from a cDNA library constructed from the spawned eggs of A. muricata. This clone was composed of 908 nucleotides, including 162 base pairs (bp) of 5′-untranslated region (UTR), 296 bp of 3′-UTR, and an open reading frame 450 bp in length. The deduced amino acid indicated that the Acropora CaM protein is identical to that of the actiniarian, Metridinium senile, and has four putative calcium-binding domains highly similar to those of other vertebrate or invertebrate CaMs. Southern blot analysis revealed that Acropora CaM is a putative single-copy gene in the nuclear genome. Genomic sequencing showed that Acropora CaM was composed of five exons and four introns, with intron II not corresponding to any region in the actiniarian CaM gene, which possesses only four exons and three introns. Our results highlight that the coral CaM gene isolated from A. muricata has four introns at the predicted positions of the early metazoan CaM gene organization, providing the first evidence from the basal eumetazoan phylum to support the four-intron hypothesis.
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References
Baba ML, Goodman M, Berger-Cohn J, Demaille JG, Matsuda G (1984) The early adaptive evolution of calmodulin. Mol Biol Evol 1:442–455
Bridge D, Cunningham CW, Schierwater B, Desalle R, Buss LW (1992) Class-level relationships in the phylum Cnidaria: evidence from mitochondrial genome structure. Proc Natl Acad Sci USA 89:8750–8753
Bridge D, Cunningham CW, DeSalle R, Buss LW (1995) Class-level relationships in the phylum Cnidaria: molecular and morphological evidence. Mol Biol Evol 12:679–689
Chen CA, Wei NV, Dai CF (2002) Genotyping the clonal population structure of a gorgonian coral, Junceella fragilis (Anthozoa: Octocorallia: Ellisellidae) from Lanyu, Taiwan, using simple sequence repeats in ribosomal intergenic spacer. Zool Stud 41:295–302
Chien YH, Dawid IB (1984) Isolation and characterization of calmodulin genes from Xenopus laevis. Mol Cell Biol 4:507–513
Davis TN, Urdea MS, Masiarz FR, Thorner J (1986) Isolation of the yeast calmodulin gene: calmodulin is an essential protein. Cell 47:423–431
Friedberg F, Rhoads AR (2001) Evolutionary aspects of calmodulin. IUBMB Life 51:215–221 [review]
Friedberg F, Rhoads AR (2002) Multiple calmodulin genes in fish. Mol Biol Rep 29:377–382
Hardy DO, Bender PK, Kretsinger RH (1988) Two calmodulin genes are expressed in Arbacia punctulata. An ancient gene duplication is indicated. J Mol Biol 199:223–227
Karabinos A, Bhattacharya D (2000) Molecular evolution of calmodulin and calmodulin-like genes in the cephalochordate Branchiostoma. J Mol Evol 51:141–148
Karabinos A, Riemer D (1997) The single calmodulin gene of the cephalochordate Branchiostoma. Gene 195:229–233
Kawasaki H, Kretsinger RH (1995) Calcium binding protein I: EF-hand. Prot Profile 2:297–490
Kawasaki H, Nakayama S, Kretsinger RH (1998) Classification and evolution of EF-hand proteins. Biometals 11:277–295
Keane TM, Naughton TJ, Travers SAA, McInerney JO, McCormack GP (2005) DPRml:distributed phylogeny reconstruction by maximum likelihood. Bioinformatics 21:969–974
Keane TM, Creevey CJ, Pentony MM, Naughton TJ, Mclnerney JO (2006) Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC Evol Biol 6:29
Koller M, Schnyder B, Strehler EE (1990) Structural organization of the human CaMIII calmodulin gene. Biochim Biophys Acta 1087:180–189
Kortschak RD, Samuel G, Saint R, Miller DJ (2003) EST analysis of the cnidarian, Acropora millepora, reveals extensive gene loss and rapid sequence divergence in the model invertebrates. Curr Biol 13:2190–2195
Kraev A, Gazzotti P (1999) Expression and functional characterization of calmodulin from Caenorhabditis elegans. GenBank/EMBL/DDBJ data banks; accession number AJ132193. Available at: http://www.ebi.ac.uk/cgi-bin/emblfetch?style=html&id=AJ132193&Submit=Go
Kretsinger RH, Nakayama S (1993) Evolution of EF-hand calcium-modulated proteins. IV. Exon shuffling did not determine the domain compositions of EF-hand proteins. J Mol Evol 36:477–488
Kumar S, Tamura K, Nei M (2004) MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5:150–163
Marshak DR, Clarke M, Roberts DM, Watterson DM (1984) Structural and functional properties of calmodulin from the eukaryotic microorganism Dictyostelium discoideum. Biochemistry 23:2891–2899
Matsuo K, Sato K, Ikeshima H, Shimoda K, Takano T (1992) Four synonymous genes encode calmodulin in the teleost fish, medaka (Oryzias latipes): conservation of the multigene one-protein principle. Gene 119:279–281
Nakayama S, Kretsinger RH (1994) Evolution of the EF-hand family of proteins. Annu Rev Biophys Biomol Struct 23:473–507
Nakayama S, Moncrief ND, Kretsinger RH (1992) Evolution of EF-hand calcium-modulated proteins. II. Domains of several subfamilies have diverse evolutionary histories. J Mol Evol 34:416–448
Nojima H (1989) Structural organization of multiple rat calmodulin genes. J Mol Biol 208:269–282
Nojima H, Sokabe H (1987) Structure of a gene for rat calmodulin. J Mol Biol 193:439–445
Raible F, Arendt D (2004) Metazoan evolution: some animals are more equal than others. Curr Biol 14:06–108
Reddy PT, Prasad CR, Reddy PH, Reeder D, McKenney K, Jaffe H, Dimitrova MN, Ginsburg A, Peterkofsky A, Murthy PS (2003) Cloning and expression of the gene for a novel protein from Mycobacterium smegmatis with functional similarity to eukaryotic calmodulin. J Bacteriol 185:5263–5268
Rhyner JA, Ottiger M, Wicki R, Greenwood TM, Strehler EE (1994) Structure of the human CALM1 calmodulin gene and identification of two CALM1-related pseudogenes CALM1P1 and CALM1P2. Eur J Biochem 225:71–82
Sarma PVGK, Sarma PU, Murthy PS (1998) Isolation, purification and characterization of intracellular calmodulin like protein (CALP) from Mycobacterium phlei. FEMS MIcrobiol Lett 159:27–34
SenGupta B, Friedberg F, Detera-Wadleigh SD (1987) Molecular analysis of human and rat calmodulin complementary DNA clones: evidence for additional active genes in these species. J Biol Chem 262:16663–16670
Simmen RC, Tanaka T, Tsui KF, Putkey JA, Scott MJ, Lai EC, Means AR (1985) The structural organization of the chicken calmodulin gene. J Biol Chem 260:907–912
Simpson RJ, Wilding CS, Grahame J. (2005) Intron analyses reveal multiple calmodulin copies in Littorina. J Mol Evol 60:505–512
Smith VL, Doyle KE, Maune JF, Munjaal RP, Beckingham K (1987) Structure and sequence of the Drosophila melanogaster calmodulin gene. J Mol Biol 196:471–485
Swan DG, Hale RS, Dhillon N, Leadlay PF (1987) A bacterial calcium-binding protein homologous to calmodulin. Nature 329:84–85
Swanson ME, Sturner SF, Schwartz JH (1990) Structure and expression of the Aplysia calfornica calmodulin gene. J Mol Biol 216:545–553
Thornton JW, Need E, Crews D (2003) Resurrecting the ancestral steroid receptor:ancient origin of estrogen signaling. Science 301:1714–1717
Toda H, Yazawa M, Kondo K, Honma T, Narita K, Yagi K (1981) Amino acid sequence of calmodulin from scallop (Patinopecten) adductor muscle. J Biochem 90:1493–1505
Wallace CC (1999) Staghorn corals of the world: a revision of the genus Acropora. CSIRO, Collingwood, Victoria, Australia
Wimmer W, Perovic S, Kruse M, Schroder HC, Krasko A, Batel R, Muller WE (1999) Origin of the integrin-mediated signal transduction. Functional studies with cell cultures from the sponge Suberites domuncula. Eur J Biochem 260:156–165
Ye Q, Berchtold MW (1997) Structure and expression of chicken calmodulin I gene. Gene 194:63–68
Yuasa HJ, Takagi T (2001) Genomic structure of the sandworm, Perinereis vancaurica tetradentata, troponin C. Gene 268:17–22
Yuasa HJ, Yamamoto H, Takagi T (1999a) The structural organization of the ascidian, Halocynthia roretzi, calmodulin genes. The vicissitude of introns during the evolution of calmodulin genes. Gene 229:163–169
Yuasa HJ, Cox JA, Takagi T (1999b) Genomic structure of the amphioxus calcium vector protein. J Biochem 126:572–577
Yuasa HJ, Suzuki T, Yazawa M (2001) Structural organization of lower marine nonvertebrate calmodulin genes. Gene 268:17–22
Acknowledgments
Many thanks to Yaoyung Chuang, Cheinwei Chen, members of the Evolutionary Ecology and Genetics of Coral Reef Laboratory (EEGCR), Research Center for Biodiversity, Academia Sinica (RCBAS), for fieldwork assistance and to the Penghu Marine Life Propagation Centre, a facility of Penghu County, for provision of the facility and hospitality during the 2005 coral spawning in Penghu. C.-Y. Chiou is the receipt of an Academia Sinica Postdoctoral Fellowship (2005–2007). N.V. Wei was supported by a predoctoral fellowship from the National Science Council (NSC), Taiwan. This work was supported by NSC grants and Academia Sinica Thematic grants (2002–2004, 2006–2007) to C.A.C. This is Evolution and Ecology Group, RCBAS, contribution no. 43.
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Chiou, CY., Chen, IP., Chen, C. et al. Analysis of Acropora muricata Calmodulin (CaM) Indicates That Scleractinian Corals Possess the Ancestral Exon/Intron Organization of the Eumetazoan CaM Gene. J Mol Evol 66, 317–324 (2008). https://doi.org/10.1007/s00239-008-9084-6
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DOI: https://doi.org/10.1007/s00239-008-9084-6