Analysis of newly established EST databases reveals similarities between heart regeneration in newt and fish

BMC Genomics

Volumn 11, Issue 1, 2010, Pages

  Borchardt, Thilo ^a   Looso, Mario ^a   Bruckskotten, Marc ^a   Weis, Patrick ^a   Kruse, Julia ^a   Braun, Thomas ^a  

^a MAX PLANCK INSTITUTE FOR HEART AND LUNG RESEARCH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL EXPERIMENT; ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; DNA LIBRARY; GENE ACTIVATION; GENETIC DATABASE; HEART; HEART INJURY; MOLECULAR CLONING; NEWT; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; SEQUENCE HOMOLOGY; TISSUE REGENERATION; UNINDEXED SEQUENCE; ZEBRA FISH; ANIMAL; CONTIG MAPPING; DNA SEQUENCE; EXPRESSED SEQUENCE TAG; GENE EXPRESSION PROFILING; GENE LIBRARY; GENETICS; PHYSIOLOGY; REGENERATION;

AMPHIBIA; DANIO RERIO; NOTOPHTHALMUS VIRIDESCENS; SALAMANDRIDAE;

ANIMALS; CONTIG MAPPING; DATABASES, GENETIC; EXPRESSED SEQUENCE TAGS; GENE EXPRESSION PROFILING; GENE LIBRARY; HEART; NOTOPHTHALMUS VIRIDESCENS; REGENERATION; SEQUENCE ANALYSIS, DNA; ZEBRAFISH;

EID: 76949094959     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-4     Document Type: Article

References (66)

1. Brockes J, Kumar A. Newts. Curr Biol 2005, 15(2):R42-44. 10.1016/j.cub.2004.12.049, 15668151.
2. Brockes JP, Kumar A. Plasticity and reprogramming of differentiated cells in amphibian regeneration. Nat Rev Mol Cell Biol 2002, 3(8):566-574. 10.1038/nrm881, 12154368.
3. Parish CL, Beljajeva A, Arenas E, Simon A. Midbrain dopaminergic neurogenesis and behavioural recovery in a salamander lesion-induced regeneration model. Development 2007, 134(15):2881-2887. 10.1242/dev.002329, 17611231.
4. Oberpriller JO, Oberpriller JC. Response of the adult newt ventricle to injury. J Exp Zool 1974, 187(2):249-253. 10.1002/jez.1401870208, 4813417.
5. Bader D, Oberpriller JO. Repair and reorganization of minced cardiac muscle in the adult newt (Notophthalmus viridescens). J Morphol 1978, 155(3):349-357. 10.1002/jmor.1051550307, 633377.
6. Borchardt T, Braun T. Cardiovascular regeneration in non-mammalian model systems: what are the differences between newts and man?. Thromb Haemost 2007, 98(2):311-318.
7. Laflamme MA, Murry CE. Regenerating the heart. Nat Biotechnol 2005, 23(7):845-856. 10.1038/nbt1117, 16003373.
8. Rubart M, Field LJ. Cardiac regeneration: repopulating the heart. Annu Rev Physiol 2006, 68:29-49. 10.1146/annurev.physiol.68.040104.124530, 16460265.
9. Rumyantsev PP. Replicative behaviour of different types of cardiomyocytes in terms of experimental conditions, age and systematic position of animals. The Development and Regenerative Potential of Cardiac Muscle 1991, 81-92. London Harwood Academic Publishers, Oberpriller JO OJ, Mauro A.
10. Soonpaa MH, Field LJ. Survey of studies examining mammalian cardiomyocyte DNA synthesis. Circ Res 1998, 83(1):15-26.
11. Bader D, Oberpriller J. Autoradiographic and electron microscopic studies of minced cardiac muscle regeneration in the adult newt, notophthalmus viridescens. J Exp Zool 1979, 208(2):177-193. 10.1002/jez.1402080206, 469482.
12. Oberpriller JO, Oberpriller JC, Arefyeva AM, Mitashov VI, Carlson BM. Nuclear characteristics of cardiac myocytes following the proliferative response to mincing of the myocardium in the adult newt, Notophthalmus viridescens. Cell Tissue Res 1988, 253(3):619-624. 10.1007/BF00219752, 3180187.
13. Laube F, Heister M, Scholz C, Borchardt T, Braun T. Re-programming of newt cardiomyocytes is induced by tissue regeneration. J Cell Sci 2006, 119(Pt 22):4719-4729. 10.1242/jcs.03252, 17077121.
14. Habermann B, Bebin AG, Herklotz S, Volkmer M, Eckelt K, Pehlke K, Epperlein HH, Schackert HK, Wiebe G, Tanaka EM. An Ambystoma mexicanum EST sequencing project: analysis of 17,352 expressed sequence tags from embryonic and regenerating blastema cDNA libraries. Genome Biol 2004, 5(9):R67. 10.1186/gb-2004-5-9-r67, 522874, 15345051.
15. Putta S, Smith JJ, Walker JA, Rondet M, Weisrock DW, Monaghan J, Samuels AK, Kump K, King DC, Maness NJ, et al. From biomedicine to natural history research: EST resources for ambystomatid salamanders. BMC Genomics 2004, 5(1):54. 10.1186/1471-2164-5-54, 509418, 15310388.
16. Samuels AK, Weisrock DW, Smith JJ, France KJ, Walker JA, Putta S, Voss SR. Transcriptional and phylogenetic analysis of five complete ambystomatid salamander mitochondrial genomes. Gene 2005, 349:43-53. 10.1016/j.gene.2004.12.037, 15780978.
17. Zhang P, Papenfuss TJ, Wake MH, Qu L, Wake DB. Phylogeny and biogeography of the family Salamandridae (Amphibia: Caudata) inferred from complete mitochondrial genomes. Mol Phylogenet Evol 2008, 49(2):586-597. 10.1016/j.ympev.2008.08.020, 18801447.
18. Monaghan JR, Epp LG, Putta S, Page RB, Walker JA, Beachy CK, Zhu W, Pao GM, Verma IM, Hunter T, et al. Microarray and cDNA sequence analysis of transcription during nerve-dependent limb regeneration. BMC Biol 2009, 7:1. 10.1186/1741-7007-7-1, 2630914, 19144100.
19. Animal Genome Size Database. , http://www.genomesize.com
20. Duellmann WE, Trueb L. Biology of Amphibians. 1994, Baltimore, Maryland: The Johns Hopkins University Press.
21. Iseli C, Jongeneel CV, Bucher P. ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proc Int Conf Intell Syst Mol Biol 1999, 138-148.
22. Abagyan RA, Batalov S. Do aligned sequences share the same fold?. J Mol Biol 1997, 273(1):355-368. 10.1006/jmbi.1997.1287, 9367768.
23. Poss KD, Wilson LG, Keating MT. Heart regeneration in zebrafish. Science 2002, 298(5601):2188-2190. 10.1126/science.1077857, 12481136.
24. Lien CL, Schebesta M, Makino S, Weber GJ, Keating MT. Gene expression analysis of zebrafish heart regeneration. PLoS Biol 2006, 4(8):e260. 10.1371/journal.pbio.0040260, 1523227,1523227, 16869712.
25. Lepilina A, Coon AN, Kikuchi K, Holdway JE, Roberts RW, Burns CG, Poss KD. A dynamic epicardial injury response supports progenitor cell activity during zebrafish heart regeneration. Cell 2006, 127(3):607-619. 10.1016/j.cell.2006.08.052, 17081981.
26. Tsonis PA. Regeneration in vertebrates. Dev Biol 2000, 221(2):273-284. 10.1006/dbio.2000.9667, 10790325.
27. BLAST2GO. , http://www.blast2go.org
28. Yasuhara N, Takeda E, Inoue H, Kotera I, Yoneda Y. Importin alpha/beta-mediated nuclear protein import is regulated in a cell cycle-dependent manner. Exp Cell Res 2004, 297(1):285-293. 10.1016/j.yexcr.2004.03.010, 15194443.
29. Umegaki N, Tamai K, Nakano H, Moritsugu R, Yamazaki T, Hanada K, Katayama I, Kaneda Y. Differential regulation of karyopherin alpha 2 expression by TGF-beta1 and IFN-gamma in normal human epidermal keratinocytes: evident contribution of KPNA2 for nuclear translocation of IRF-1. J Invest Dermatol 2007, 127(6):1456-1464. 10.1038/sj.jid.5700716, 17255955.
30. Mita AC, Mita MM, Nawrocki ST, Giles FJ. Survivin: key regulator of mitosis and apoptosis and novel target for cancer therapeutics. Clin Cancer Res 2008, 14(16):5000-5005. 10.1158/1078-0432.CCR-08-0746, 18698017.
31. Wang J, Yang L, Yang J, Kuropatwinski K, Wang W, Liu XQ, Hauser J, Brattain MG. Transforming growth factor beta induces apoptosis through repressing the phosphoinositide 3-kinase/AKT/survivin pathway in colon cancer cells. Cancer Res 2008, 68(9):3152-3160. 10.1158/0008-5472.CAN-07-5348, 18451140.
32. Xia F, Canovas PM, Guadagno TM, Altieri DC. A survivin-ran complex regulates spindle formation in tumor cells. Mol Cell Biol 2008, 28(17):5299-5311. 10.1128/MCB.02039-07, 2519733, 18591255.
33. Shannan B, Seifert M, Boothman DA, Tilgen W, Reichrath J. Clusterin and DNA repair: a new function in cancer for a key player in apoptosis and cell cycle control. J Mol Histol 2006, 37(5-7):183-188. 10.1007/s10735-006-9052-7, 17048076.
34. Trougakos IP, Djeu JY, Gonos ES, Boothman DA. Advances and challenges in basic and translational research on clusterin. Cancer Res 2009, 69(2):403-406. 10.1158/0008-5472.CAN-08-2912, 19147550.
35. Shannan B, Seifert M, Leskov K, Willis J, Boothman D, Tilgen W, Reichrath J. Challenge and promise: roles for clusterin in pathogenesis, progression and therapy of cancer. Cell Death Differ 2006, 13(1):12-19. 10.1038/sj.cdd.4401779, 16179938.
36. Baumgrass R, Zhang Y, Erdmann F, Thiel A, Weiwad M, Radbruch A, Fischer G. Substitution in position 3 of cyclosporin A abolishes the cyclophilin-mediated gain-of-function mechanism but not immunosuppression. J Biol Chem 2004, 279(4):2470-2479. 10.1074/jbc.M304754200, 14583619.
37. Tropschug M, Barthelmess IB, Neupert W. Sensitivity to cyclosporin A is mediated by cyclophilin in Neurospora crassa and Saccharomyces cerevisiae. Nature 1989, 342(6252):953-955. 10.1038/342953a0, 2531848.
38. Semba S, Huebner K. Protein expression profiling identifies cyclophilin A as a molecular target in Fhit-mediated tumor suppression. Mol Cancer Res 2006, 4(8):529-538. 10.1158/1541-7786.MCR-06-0060, 16885564.
39. Rensen WM, Mangiacasale R, Ciciarello M, Lavia P. The GTPase Ran: regulation of cell life and potential roles in cell transformation. Front Biosci 2008, 13:4097-4121. 10.2741/2996, 18508502.
40. Clarke PR, Zhang C. Spatial and temporal coordination of mitosis by Ran GTPase. Nat Rev Mol Cell Biol 2008, 9(6):464-477. 10.1038/nrm2410, 18478030.
41. Ho MS, Tsai PI, Chien CT. F-box proteins: the key to protein degradation. J Biomed Sci 2006, 13(2):181-191. 10.1007/s11373-005-9058-2, 16463014.
42. Chew EH, Hagen T. Substrate-mediated regulation of cullin neddylation. J Biol Chem 2007, 282(23):17032-17040. 10.1074/jbc.M701153200, 17439941.
43. Zhang YZ, Gould KL, Dunbrack RJ, Cheng H, Roder H, Golemis EA. The evolutionarily conserved Dim1 protein defines a novel branch of the thioredoxin fold superfamily. Physiol Genomics 1999, 1(3):109-118.
44. Zhang Y, Lindblom T, Chang A, Sudol M, Sluder AE, Golemis EA. Evidence that dim1 associates with proteins involved in pre-mRNA splicing, and delineation of residues essential for dim1 interactions with hnRNP F and Npw38/PQBP-1. Gene 2000, 257(1):33-43. 10.1016/S0378-1119(00)00372-3, 11054566.
45. Parish JL, Rosa J, Wang X, Lahti JM, Doxsey SJ, Androphy EJ. The DNA helicase ChlR1 is required for sister chromatid cohesion in mammalian cells. J Cell Sci 2006, 119(Pt 23):4857-4865. 10.1242/jcs.03262, 17105772.
46. Inoue A, Li T, Roby SK, Valentine MB, Inoue M, Boyd K, Kidd VJ, Lahti JM. Loss of ChlR1 helicase in mouse causes lethality due to the accumulation of aneuploid cells generated by cohesion defects and placental malformation. Cell Cycle 2007, 6(13):1646-1654.
47. Lyapina SA, Correll CC, Kipreos ET, Deshaies RJ. Human CUL1 forms an evolutionarily conserved ubiquitin ligase complex (SCF) with SKP1 and an F-box protein. Proc Natl Acad Sci USA 1998, 95(13):7451-7456. 10.1073/pnas.95.13.7451, 22647, 9636170.
48. Lehmann A, Toda T. Fission yeast Skp1 is required for spindle morphology and nuclear membrane segregation at anaphase. FEBS Lett 2004, 566(1-3):77-82. 10.1016/j.febslet.2004.04.022, 15147872.
49. Kiat LS, Hui KM, Gopalan G. Aurora-A kinase interacting protein (AIP), a novel negative regulator of human Aurora-A kinase. J Biol Chem 2002, 277(47):45558-45565. 10.1074/jbc.M206820200, 12244051.
50. Fumoto K, Lee PC, Saya H, Kikuchi A. AIP regulates stability of Aurora-A at early mitotic phase coordinately with GSK-3beta. Oncogene 2008, 27(32):4478-4487. 10.1038/onc.2008.92, 18391981.
51. Middendorp S, Kuntziger T, Abraham Y, Holmes S, Bordes N, Paintrand M, Paoletti A, Bornens M. A role for centrin 3 in centrosome reproduction. J Cell Biol 2000, 148(3):405-416. 10.1083/jcb.148.3.405, 2174797, 10662768.
52. Salisbury JL, Suino KM, Busby R, Springett M. Centrin-2 is required for centriole duplication in mammalian cells. Curr Biol 2002, 12(15):1287-1292. 10.1016/S0960-9822(02)01019-9, 12176356.
53. Graidist P, Yazawa M, Tonganunt M, Nakatomi A, Lin CC, Chang JY, Phongdara A, Fujise K. Fortilin binds Ca2+ and blocks Ca2+-dependent apoptosis in vivo. Biochem J 2007, 408(2):181-191. 10.1042/BJ20070679, 2267342, 17705784.
54. Chen SH, Wu PS, Chou CH, Yan YT, Liu H, Weng SY, Yang-Yen HF. A knockout mouse approach reveals that TCTP functions as an essential factor for cell proliferation and survival in a tissue- or cell type-specific manner. Mol Biol Cell 2007, 18(7):2525-2532. 10.1091/mbc.E07-02-0188, 1924818, 17475776.
55. Kawano Y, Kypta R. Secreted antagonists of the Wnt signalling pathway. J Cell Sci 2003, 116(Pt 13):2627-2634. 10.1242/jcs.00623, 12775774.
56. Swaroop M, Gosink M, Sun Y. SAG/ROC2/Rbx2/Hrt2, a component of SCF E3 ubiquitin ligase: genomic structure, a splicing variant, and two family pseudogenes. DNA Cell Biol 2001, 20(7):425-434. 10.1089/104454901750361488, 11506706.
57. Jiang W, Bell CW, Pisetsky DS. The relationship between apoptosis and high-mobility group protein 1 release from murine macrophages stimulated with lipopolysaccharide or polyinosinic-polycytidylic acid. J Immunol 2007, 178(10):6495-6503.
58. De Mori R, Straino S, Di Carlo A, Mangoni A, Pompilio G, Palumbo R, Bianchi ME, Capogrossi MC, Germani A. Multiple effects of high mobility group box protein 1 in skeletal muscle regeneration. Arterioscler Thromb Vasc Biol 2007, 27(11):2377-2383. 10.1161/ATVBAHA.107.153429, 17872450.
59. Germani A, Limana F, Capogrossi MC. Pivotal advances: high-mobility group box 1 protein--a cytokine with a role in cardiac repair. J Leukoc Biol 2007, 81(1):41-45. 10.1189/jlb.0306165, 16940333.
60. Agrawal PB, Greenleaf RS, Tomczak KK, Lehtokari VL, Wallgren-Pettersson C, Wallefeld W, Laing NG, Darras BT, Maciver SK, Dormitzer PR, et al. Nemaline myopathy with minicores caused by mutation of the CFL2 gene encoding the skeletal muscle actin-binding protein, cofilin-2. Am J Hum Genet 2007, 80(1):162-167. 10.1086/510402, 1785312, 17160903.
61. Flores-Delgado G, Liu CW, Sposto R, Berndt N. A limited screen for protein interactions reveals new roles for protein phosphatase 1 in cell cycle control and apoptosis. J Proteome Res 2007, 6(3):1165-1175. 10.1021/pr060504h, 17274640.
62. Birkenfeld J, Betz H, Roth D. Identification of cofilin and LIM-domain-containing protein kinase 1 as novel interaction partners of 14-3-3 zeta. Biochem J 2003, 369(Pt 1):45-54. 10.1042/BJ20021152, 1223062, 12323073.
63. Arber S, Hunter JJ, Ross J, Hongo M, Sansig G, Borg J, Perriard JC, Chien KR, Caroni P. MLP-deficient mice exhibit a disruption of cardiac cytoarchitectural organization, dilated cardiomyopathy, and heart failure. Cell 1997, 88(3):393-403. 10.1016/S0092-8674(00)81878-4, 9039266.
64. Heineke J, Ruetten H, Willenbockel C, Gross SC, Naguib M, Schaefer A, Kempf T, Hilfiker-Kleiner D, Caroni P, Kraft T, et al. Attenuation of cardiac remodeling after myocardial infarction by muscle LIM protein-calcineurin signaling at the sarcomeric Z-disc. Proc Natl Acad Sci USA 2005, 102(5):1655-1660. 10.1073/pnas.0405488102, 547821, 15665106.
65. Batta K, Kundu TK. Activation of p53 function by human transcriptional coactivator PC4: role of protein-protein interaction, DNA bending, and posttranslational modifications. Mol Cell Biol 2007, 27(21):7603-7614. 10.1128/MCB.01064-07, 2169069, 17785449.
66. Vadivelu SK, Kurzbauer R, Dieplinger B, Zweyer M, Schafer R, Wernig A, Vietor I, Huber LA. Muscle regeneration and myogenic differentiation defects in mice lacking TIS7. Mol Cell Biol 2004, 24(8):3514-3525. 10.1128/MCB.24.8.3514-3525.2004, 381666, 15060170.