Genomic organization, expression, and phylogenetic analysis of Ca 2+ channel β4 genes in 13 vertebrate species

Physiological Genomics

Volumn 35, Issue 2, 2008, Pages 133-144

  Ebert, Alicia M ^a   McAnelly, Catherine A ^a   Handschy, Anne V ^a   Mueller, Rachel Lockridge ^a   Horne, William A ^b   Garrity, Deborah M ^a  

^a Department of Environmental and Radiological Health Sciences   (United States)

^b Department of Obstetrics Gynecology   (United States)

Author keywords

subunit; Development; Expression; Heart; Membrane associated guanylate kinase; Nervous system; Splicing; Zebrafish

Indexed keywords

BETA4 PROTEIN; CALCIUM CHANNEL; CALCIUM CHANNEL BETA2; COMPLEMENTARY DNA; MEMBRANE ASSOCIATED GUANYLATE CYCLASE KINASE; NEUROGENIC DIFFERENTIATION FACTOR; NUCLEIC ACID BINDING PROTEIN; UNCLASSIFIED DRUG; VOLTAGE GATED CALCIUM CHANNEL;

ALTERNATIVE RNA SPLICING; ANIMAL EXPERIMENT; ARTICLE; BETA CHAIN; BRAIN DEVELOPMENT; CHANNEL GATING; CONVERGENT EVOLUTION; EMBRYO; EMBRYO DEVELOPMENT; EXON; GENE DUPLICATION; GENE EXPRESSION; GENE SEQUENCE; GENETIC ORGANIZATION; GENETIC VARIABILITY; GENOME; GENOMICS; INTRON; NERVOUS SYSTEM DEVELOPMENT; NONHUMAN; NUCLEOTIDE SEQUENCE; PARALOGY; PHENOTYPE; PHYLOGENY; PRIORITY JOURNAL; PROTEIN DOMAIN; SPATIAL DISCRIMINATION; TELEOST; TIME PERCEPTION; VERTEBRATE; ZEBRA FISH;

ALTERNATIVE SPLICING; AMINO ACID SEQUENCE; ANIMALS; CALCIUM CHANNELS; EVOLUTION, MOLECULAR; GENE EXPRESSION; GENOME; GENOMICS; HUMANS; IN SITU HYBRIDIZATION; INTRONS; MOLECULAR SEQUENCE DATA; PHYLOGENY; PROTEIN SUBUNITS; RNA, MESSENGER; SEQUENCE ALIGNMENT; VERTEBRATES; ZEBRAFISH;

DANIO RERIO; TELEOSTEI; TETRAPODA; VERTEBRATA;

EID: 57049187897     PISSN: 10948341     EISSN: 15312267     Source Type: Journal    
DOI: 10.1152/physiolgenomics.90264.2008     Document Type: Article

References (74)

1. The Fugu Genome Project Database [http://www.fugu-sg.org/].
2. The JGI Eukaryotic Genomes Databases [http://genome.jgi-psf.org/].
3. The National Center for Biotechnology Information Entrez Database [http://www.ncbi.nlm.nih.gov/sites/gquery].
4. The Sanger Center Ensembl Databases [http://www.ensembl.org/index.html].
5. The Tetraodon Genome Browser [http://www.genoscope.cns.fr/externe/ tetranew/].
6. The UCSC Genome Bioinformatics Databases [http://genome.ucsc.edu/].
7. Acosta L, Haase H, Morano I, Moorman AF, Franco D. Regional expression of L-type calcium channel subunits during cardiac development. Dev Dyn 230: 131-136, 2004.
8. Aparicio S, Chapman J, Stupka E, Putnam N, Chia JM, Dehal P, Christoffels A, Rash S, Hoon S, Smit A, Gelpke MD, Roach J, Oh T, Ho IY, Wong M, Detter C, Verhoef F, Predki P, Tay A, Lucas S, Richardson P, Smith SF, Clark MS, Edwards YJ, Doggett N, Zharkikh A, Tavtigian SV, Pruss D, Barnstead M, Evans C, Baden H, Powell J, Glusman G, Rowen L, Hood L, Tan YH, Elgar G, Hawkins T, Venkatesh B, Rokhsar D, Brenner S. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297: 1301-1310, 2002.
9. Avanzini G, Franceschetti S, Mantegazza M. Epileptogenic channelopathies: experimental models of human pathologies. Epilepsia 48: 51-64, 2007.
10. Badou A, Basavappa S, Desai R, Peng YQ, Matza D, Mehal WZ, Kaczmarek LK, Boulpaep EL, Flavell RA. Requirement of voltage-gated calcium channel beta4 subunit for T lymphocyte functions. Science 307: 117-121, 2005.
11. Ball SL, Powers PA, Shin HS, Morgans CW, Peachey NS, Gregg RG. Role of the beta(2) subunit of voltage-dependent calcium channels in the retinal outer plexiform layer. Invest Ophthalmol Vis Sci 43: 1595-1603, 2002.
12. Bally-Cuif L. Breaking symmetry on time. Dev Cell 12: 1-2, 2007.
13. Benton MJ, Donoghue PC. Paleontological evidence to date the tree of life. Mol Biol Evol 24: 26-53, 2007.
14. Bernard G, Shevell MI. Channelopathies: a review. Pediatr Neurol 38: 73-85, 2008.
15. 2+ channel alpha1 subunit contains an endoplasmic reticulum retention signal antagonized by the beta subunit. Neuron 25: 177-190, 2000.
16. Bilotta J, Saszik S. The zebrafish as a model visual system. Int J Dev Neurosci 19: 621-629, 2001.
17. Bogdanov Y, Brice NL, Canti C, Page KM, Li M, Volsen SG, Dolphin AC. Acidic motif responsible for plasma membrane association of the voltage-dependent calcium channel beta1b subunit. Eur J Neurosci 12: 894-902, 2000.
18. Brice NL, Berrow NS, Campbell V, Page KM, Brickley K, Tedder I, Dolphin AC. Importance of the different beta subunits in the membrane expression of the alpha1A and alpha2 calcium channel subunits: studies using a depolarization-sensitive alpha1A antibody. Eur J Neurosci 9: 749-759, 1997.
19. Brice NL, Dolphin AC. Differential plasma membrane targeting of voltage-dependent calcium channel subunits expressed in a polarized epithelial cell line. J Physiol 515: 685-694, 1999.
20. 2+ channel beta subunit gene Cchb4 is associated with ataxia and seizures in the lethargic (lh) mouse. Cell 88: 385-392, 1997.
21. Burns CG, Milan DJ, Grande EJ, Rottbauer W, MacRae CA, Fishman MC. High-throughput assay for small molecules that modulate zebrafish embryonic heart rate. Nat Chem Biol 1: 263-264, 2005.
22. Chen YH, Li MH, Zhang Y, He LL, Yamada Y, Fitzmaurice A, Shen Y, Zhang H, Tong L, Yang J. Structural basis of the alpha1-beta subunit interaction of voltage-gated Ca2+ channels. Nature 429: 675-680, 2004.
23. Chin H, Kwon OJ, Jung HH, Kim DS, Kozak CA. Genetic mapping of the mouse genes encoding the voltage-sensitive calcium channel subunits. Genomics 28: 592-595, 1995.
24. Chu PJ, Larsen JK, Chen CC, Best PM. Distribution and relative expression levels of calcium channel beta subunits within the chambers of the rat heart. J Mol Cell Cardiol 36: 423-434, 2004.
25. Colecraft HM, Alseikhan B, Takahashi SX, Chaudhuri D, Mittman S, Yegnasubramanian V, Alvania RS, Johns DC, Marban E, Yue DT. Novel functional properties of Ca(2+) channel beta subunits revealed by their expression in adult rat heart cells. J Physiol 541: 435-452, 2002.
26. Cork RJ, Namkung Y, Shin HS, Mize RR. Development of the visual pathway is disrupted in mice with a targeted disruption of the calcium channel beta(3)-subunit gene. J Comp Neurol 440: 177-191, 2001.
27. Dalton S, Takahashi SX, Miriyala J, Colecraft HM. A single CaVbeta can reconstitute both trafficking and macroscopic conductance of voltage-dependent calcium channels. J Physiol 567: 757-769, 2005.
28. Ebert A, McAnelly C, Srinivasan A, Mueller R, Garrity D, Garrity D. The calcium channel β2 (CACNB2) subunit repertoire in teleosts. BMC Mol Biol 9: 38, 2008.
29. Ebert AM, McAnelly CA, Srinivasan A, Linker JL, Horne WA, Garrity DM. Ca2+ channel-independent requirement for MAGUK family CACNB4 genes in initiation of zebrafish epiboly. Proc Natl Acad Sci USA 105: 198-203, 2008.
30. Escayg A, De Waard M, Lee DD, Bichet D, Wolf P, Mayer T, Johnston J, Baloh R, Sander T, Meisler MH. Coding and noncoding variation of the human calcium-channel beta4-subunit gene CACNB4 in patients with idiopathic generalized epilepsy and episodic ataxia. Am J Hum Genet 66: 1531-1539, 2000.
31. Escayg A, Jones JM, Kearney JA, Hitchcock PF, Meisler MH. Calcium channel beta 4 (CACNB4): human ortholog of the mouse epilepsy gene lethargic. Genomics 50: 14-22, 1998.
32. Force A, Lynch M, Pickett FB, Amores A, Yan YL, Postlethwait J. Preservation of duplicate genes by complementary, degenerative mutations. Genetics 151: 1531-1545, 1999.
33. Gates MA, Kim L, Egan ES, Cardozo T, Sirotkin HI, Dougan ST, Lashkari D, Abagyan R, Schier AF, Talbot WS. A genetic linkage map for zebrafish: comparative analysis and localization of genes and expressed sequences. Genome Res 9: 334-347, 1999.
34. Gonzalez-Gutierrez G, Miranda-Laferte E, Neely A, Hidalgo P. The SRC homology 3 domain of the beta-subunit of voltage-gated calcium channels promotes endocytosis via dynamin interaction. J Biol Chem 282: 2156-2162, 2007.
35. Haase H, Pfitzmaier B, McEnery MW, Morano I. Expression of Ca(2+) channel subunits during cardiac ontogeny in mice and rats: identification of fetal alpha(1C) and beta subunit isoforms. J Cell Biochem 76: 695-703, 2000.
36. 2+ channels. J Neurosci 22: 9331-9339, 2002.
37. 2+-channel beta 4 subunit. Proc Natl Acad Sci USA 100: 307-312, 2003.
38. Hidalgo P, Neely A. Multiplicity of protein interactions and functions of the voltage-gated calcium channel beta-subunit. Cell Calcium 42: 389-396, 2007.
39. Hong X, Scofield DG, Lynch M. Intron size, abundance, and distribution within untranslated regions of genes. Mol Biol Evol 23: 2392-2404, 2006.
40. Hsueh YP. The role of the MAGUK protein CASK in neural development and synaptic function. Curr Med Chem 13: 1915-1927, 2006.
41. Hullin R, Khan IF, Wirtz S, Mohacsi P, Varadi G, Schwartz A, Herzig S. Cardiac L-type calcium channel beta-subunits expressed in human heart have differential effects on single channel characteristics. J Biol Chem 278: 21623-21630, 2003.
42. Hurley IA, Mueller RL, Dunn KA, Schmidt EJ, Friedman M, Ho RK, Prince VE, Yang Z, Thomas MG, Coates MI. A new time-scale for ray-finned fish evolution. Proc Biol Sci 274: 489-498, 2007.
43. Kimmel C, Ballard W, Kimmel S, Ullmann B, Schilling T. Stages of embryonic development of the zebrafish. Dev Dyn 203: 253-310, 1995.
44. Le Hir H, Nott A, Moore MJ. How introns influence and enhance eukaryotic gene expression. Trends Biochem Sci 28: 215-220, 2003.
45. Ludwig A, Flockerzi V, Hofmann F. Regional expression and cellular localization of the alpha1 and beta subunit of high voltage-activated calcium channels in rat brain. J Neurosci 17: 1339-1349, 1997.
46. Marmorstein LY, Wu J, McLaughlin P, Yocom J, Karl MO, Neussert R, Wimmers S, Stanton JB, Gregg RG, Strauss O, Peachey NS, Marmorstein AD. The light peak of the electroretinogram is dependent on voltage-gated calcium channels and antagonized by bestrophin (best-1). J Gen Physiol 127: 577-589, 2006.
47. McEnery MW, Vance CL, Begg CM, Lee WL, Choi Y, Dubel SJ. Differential expression and association of calcium channel subunits in development and disease. J Bioenerg Biomembr 30: 409-418, 1998.
48. Nott A, Meislin SH, Moore MJ. A quantitative analysis of intron effects on mammalian gene expression. RNA 9: 607-617, 2003.
49. Ohno S. Evolution by Gene Duplication. Heidelberg, Germany: Springer Verlag, 1970.
50. Ohtsuka Y, Okamura Y. Voltage-dependent calcium influx mediates maturation of myofibril arrangement in ascidian larval muscle. Dev Biol 301: 361-373, 2007.
51. Perez-Reyes E, Castellano A, Kim HS, Bertrand P, Baggstrom E, Lacerda AE, Wei XY, Birnbaumer L. Cloning and expression of a cardiac/brain beta subunit of the L-type calcium channel. J Biol Chem 267: 1792-1797, 1992.
52. Postlethwait J, Amores A, Cresko W, Singer A, Yan YL. Subfunction partitioning, the teleost radiation and the annotation of the human genome. Trends Genet 20: 481-490, 2004.
53. Postlethwait JH, Woods IG, Ngo-Hazelett P, Yan YL, Kelly PD, Chu F, Huang H, Hill-Force A, Talbot WS. Zebrafish comparative genomics and the origins of vertebrate chromosomes. Genome Res 10: 1890-1902, 2000.
54. Pragnell M, De Waard M, Mori Y, Tanabe T, Snutch TP, Campbell KP. Calcium channel beta-subunit binds to a conserved motif in the I-II cytoplasmic linker of the alpha 1-subunit. Nature 368: 67-70, 1994.
55. Prince V. The Hox Paradox: more complex(es) than imagined. Dev Biol 249: 1-15, 2002.
56. 2+ channel beta subunits? Sci STKE 2005: pe11, 2005.
57. Sakharkar MK, Chow VT, Kangueane P. Distributions of exons and introns in the human genome. In Silico Biol 4: 387-393, 2004.
58. Schmitt EA, Dowling JE. Early retinal development in the zebrafish, Danio rerio: light and electron microscopic analyses. J Comp Neurol 404: 515-536, 1999.
59. Semon M, Wolfe KH. Reciprocal gene loss between Tetraodon and zebrafish after whole genome duplication in their ancestor. Trends Genet 23: 108-112, 2007.
60. Sutherland RJ. The dorsal diencephalic conduction system: a review of the anatomy and functions of the habenular complex. Neurosci Biobehav Rev 6: 1-13, 1982.
61. Takahashi SX, Mittman S, Colecraft HM. Distinctive modulatory effects of five human auxiliary beta2 subunit splice variants on L-type calcium channel gating. Biophys J 84: 3007-3021, 2003.
62. Tanaka O, Sakagami H, Kondo H. Localization of mRNAs of voltage-dependent Ca(2+)-channels: four subtypes of alpha 1- and beta-subunits in developing and mature rat brain. Brain Res Mol Brain Res 30: 1-16, 1995.
63. Tareilus E, Roux M, Qin N, Olcese R, Zhou J, Stefani E, Birnbaumer L. A Xenopus oocyte beta subunit: evidence for a role in the assembly/expression of voltage-gated calcium channels that is separate from its role as a regulatory subunit. Proc Natl Acad Sci USA 94: 1703-1708, 1997.
64. Taviaux S, Williams ME, Harpold MM, Nargeot J, Lory P. Assignment of human genes for beta 2 and beta 4 subunits of voltage-dependent Ca2+ channels to chromosomes 10p12 and 2q22-q23. Hum Genet 100: 151-154, 1997.
65. Taylor JS, Raes J. Duplication and divergence: the evolution of new genes and old ideas. Annu Rev Genet 38: 615-643, 2004.
66. Thisse B, Thisse C. Fast release clones: a high throughout expression analysis. ZFIN Direct Data Submission (http://zfin.org).
67. Thisse C, Thisse B, Schilling TF, Postlethwait JH. Structure of the zebrafish snail1 gene and its expression in wild-type, spadetail and no tail mutant embryos. Development 119: 1203-1215, 1993.
68. Van Petegem F, Clark KA, Chatelain FC, Minor DL Jr. Structure of a complex between a voltage-gated calcium channel beta-subunit and an alpha-subunit domain. Nature 429: 671-675, 2004.
69. Vance CL, Begg CM, Lee WL, Haase H, Copeland TD, McEnery MW. Differential expression and association of calcium channel alpha1B and beta subunits during rat brain ontogeny. J Biol Chem 273: 14495-14502, 1998.
70. 2+ channel beta4a subunit. Protein Sci 15: 378-383, 2006.
71. Volff JN. Genome evolution and biodiversity in teleost fish. Heredity 94: 280-294, 2005.
72. 2+ current in Cav(beta)2-/- embryos impairs cardiac development and contraction with secondary defects in vascular maturation. Circ Res 99: 749-757, 2006.
73. 2+ exchanger by polymerase chain reaction. Am J Physiol Renal Fluid Electrolyte Physiol 263: F680-F685, 1992.
74. Zhou W, Saint-Amant L, Hirata H, Cui WW, Sprague SM, Kuwada JY. Nonsense mutations in the dihydropyridine receptor beta1 gene, CACNB1, paralyze zebrafish relaxed mutants. Cell Calcium 39: 227-236, 2006.