Isolation, characterization and comparison of Atlantic and Chinook salmon growth hormone 1 and 2
详细信息 查看全文
- 作者：Kristian R von Schalburg (1)
Ryosuke Yazawa (1)
Johan de Boer (1)
Krzysztof P Lubieniecki (2)
Benjamin Goh (3)
Christopher A Straub (1)
Marianne R Beetz-Sargent (1)
Adrienne Robb (1)
William S Davidson (2)
Robert H Devlin (3)
Ben F Koop (1) - 刊名：BMC Genomics
- 出版年：2008
- 出版时间：December 2008
- 年：2008
- 卷：9
- 期：1
- 全文大小：652KB
- 参考文献：1. Thorgaard GH, Bailey GS, Williams D, Buhler DR, Kaattari SL, Ristow SS, Hansen JD, Winton JR, Bartholomew JL, Nagler JJ, Walsh PJ, Vijayan MM, Devlin RH, Hardy RW, Overturf KE, Young WP, Robison BD, Rexroad C, Palti Y: Status and opportunities for genomics research with rainbow trout. / Comp Biochem Physiol B Biochem Mol Biol 2002, 133:609鈥?46. CrossRef
2. Groot C, Margolis L: / Pacific Salmon Life Histories Vancouver, Canada: UBC Press 1991.
3. Groot C, Margolis L, Clarke WC: / Physiological Ecology of Pacific Salmon Vancouver, Canada: UBC Press 1995.
4. Thompson BJL, Shang CA, Waters MJ: Identification of genes induced by growth hormone in rat liver using cDNA arrays. / Endocrinology 2000, 141:4321鈥?324. CrossRef
5. Bjornsson BTh: The biology of salmon growth hormone: from daylight to dominance. / Fish Physiol Biochem 1997, 17:9鈥?4. CrossRef
6. Kraak G, Rosenblum PM, Peter RE: Growth hormone-dependent potentiation of gonadotropin-stimulated steroid production by ovarian follicles of the goldfish. / Gen Comp Endocr 1990, 79:233鈥?39. CrossRef
7. Sakamoto T, Hirano T: Expression of insulin-like growth factor I gene in osmoregulatory organs during seawater adaptation of the salmonid fish: Possible mode of osmoregulatory action of growth hormone. / Proc Natl Acad Sci USA 1993, 90:1912鈥?916. CrossRef
8. McKay SJ, Trautner J, Smith MJ, Koop BF, Devlin RH: Evolution of duplicated growth hormone genes in autotetraploid salmonid fishes. / Genome 2004, 47:714鈥?23. CrossRef
9. Devlin RH: Sequence of sockeye salmon type 1 and 2 growth hormone genes and the relationship of rainbow trout with Atlantic and Pacific salmon. / Can J Fish Aquat Sci 1993, 50:1738鈥?748. CrossRef
10. Very NM, Kittilson JD, Norbeck LA, Sheridan MA: Isolation, characterization, and distribution of two cDNAs encoding for growth hormone receptor in rainbow trout ( Oncorhynchus mykiss ). / Comp Biochem Physiol B 2005, 140:615鈥?28. CrossRef
11. Baudet ML, Martin B, Hassanali Z, Parker E, Sanders EJ, Harvey S: Expression, translation and localization of a novel, small growth hormone variant. / Endocrinology 2007, 148:103鈥?15. CrossRef
12. Mori T, Devlin RH: Transgene and host GH gene expression in pituitary and nonpituitary tissues of normal and GH transgenic salmon. / Mol Cell Endocrinol 1999, 149:129鈥?39. CrossRef
13. Yada T, Azuma T: Hypophysectomy depresses immune functions in rainbow trout. / Comp Biochem Physiol C 2002, 131:93鈥?00.
14. iCE - internet Contig Explorer [http://www.bcgsc.ca/platform/bioinfo/software/ice]
15. DIGIT - Digit Integrated Gene Identification Tools [http://digit.gsc.riken.jp/cgi-bin/index.cgi]
16. Altschul SF, Madden TL, Sch盲ffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. / Nucleic Acids Res 1997, 25:3389鈥?402. CrossRef
17. Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I: VISTA: computational tools for comparative genomics. / Nucleic Acids Res 2004, 32:W273鈥?79. CrossRef
18. RepeatMasker Open - 3.0 [http://www.repeatmasker.org]
19. de Boer JG, Yazawa R, Davidson WS, Koop BF: Bursts and horizontal evolution of DNA transposons in the speciation of pseudotetraploid salmonids. / BMC Genomics 2007, 8:422鈥?31. CrossRef
20. Lukacs MF, Harstad H, Grimholt U, Beetz-Sargent M, Cooper GA, Reid L, Bakke HG, Phillips RB, Miller KM, Davidson WS, Koop BF: Genomic organization of duplicated major histocompatibility complex class I regions in Atlantic salmon ( Salmo salar ). / BMC Genomics 2007, 8:251鈥?66. CrossRef
21. Kapitonov VV, Jurka J: Self-synthesizing DNA transposons in eukaryotes. / Proc Natl Acad Sci USA 2006, 103:4540鈥?545. CrossRef
22. Argenton F, Vianello S, Bernardini S, Lopreiato R, Colombo L, Bortolussi M: Trout GH promoter analysis reveals a modular pattern of regulation consistent with the diversification of GH gene control and function in vertebrates. / Mol Cell Endocrinol 2002, 189:11鈥?3. CrossRef
23. Wong AOL, Le Drean Y, Liu D, Hu ZZ, Du SJ, Hew CL: Induction of Chinook salmon growth hormone promoter activity by the adenosine 3',5'-monophosphate (cAMP)-dependent pathway involves two cAMP-response elements with the CGTCA motif and the pituitary-specific transcription factor Pit-1. / Endocrinology 1996, 137:1775鈥?784. CrossRef
24. Andersen B, Rosenfeld MG: Pit-1 determines cell types during development of the anterior pituitary gland. / J Biol Chem 1994, 269:29335鈥?9338.
25. Lehmann M: Anything else but GAGA: a nonhistone protein complex reshapes chromatin structure. / Trends Genet 2004, 20:15鈥?2. CrossRef
26. Chapman BA, Bowers JE, Feltus FA, Paterson AH: Buffering of crucial functions by paleologous duplicated genes may contribute cyclicality to angiosperm genome duplication. / Proc Natl Acad Sci USA 2006, 103:2730鈥?735. CrossRef
27. Lynch M, Force A: The probability of duplicate gene preservation by subfunctionalization. / Genetics 2000, 154:459鈥?73.
28. Yada T, Muto K, Azuma T, Hyodo S, Schreck CB: Cortisol stimulates growth hormone gene expression in rainbow trout leucocytes in vitro. / Gen Comp Endocrinol 2005, 142:248鈥?55. CrossRef
29. Bergan V, Steinsvik S, Xu H, Kileng O, Robertsen B: Promoters of type 1 interferon genes from Atlantic salmon contain two main regulatory regions. / FEBS Journal 2006, 273:3893鈥?906. CrossRef
30. Novak AE, Jost MC, Lu Y, Taylor AD, Zakon HH, Ribera AB: Gene duplications and evolution of vertebrate voltage-gated sodium channels. / J Mol Evol 2006, 63:208鈥?21. CrossRef
31. Fugu Genomics Project [http://fugu.biology.qmul.ac.uk]
32. Novak AE, Taylor AD, Pineda RH, Lasda EL, Wright MA, Ribera AB: Embryonic and larval expression of zebrafish voltage-gated sodium channel alpha-subunit genes. / Dev Dyn 2006, 235:1962鈥?973. CrossRef
33. Zebrafish Genome Resources [http://www.ncbi.nlm.nih.gov/genome/guide/zebrafish]
34. Du SJ, Devlin RH, Hew CL: Genomic structure of growth hormone genes in Chinook salmon ( Oncorhynchus tshawytscha ): presence of two functional genes, GH-I and GH-II, and a male-specific pseudogene, GH-psi. / DNA Cell Biol 1993, 12:739鈥?51. CrossRef
35. Devlin RH, Biagi CA, Smailus DE: Genetic mapping of Y-chromosomal DNA markers in Pacific salmon. / Genetica 2001, 111:43鈥?8. CrossRef
36. Coe IR, von Schalburg KR, Sherwood NM: Characterization of the Pacific salmon gonadotropin-releasing hormone gene, copy number and transcriptional start site. / Mol Cell Endocrinol 1995, 115:113鈥?22. CrossRef
37. Simons C, Pheasant M, Makunin IV, Mattick JS: Transposon-free regions in mammalian genomes. / Genome Res 2006, 16:164鈥?72. CrossRef
38. Simons C, Makunin IV, Pheasant M, Mattick JS: Maintenance of transposon-free regions throughout vertebrate evolution. / BMC Genomics 2007, 8:470鈥?79. CrossRef
39. Allendorf FW, Thorgaard GH: Tetraploidy and the evolution of salmonid fishes. / Evolutionary Genetics of Fishes / (Edited by: Turner BJ). New York: Plenum Press 1984, 1鈥?3.
40. Hoegg S, Brinkmann H, Taylor JS, Meyer A: Phylogenetic timing of the fish-specific genome duplication correlates with the diversification of teleost fish. / J Mol Evol 2004, 59:190鈥?03. CrossRef
41. McKay SJ, Devlin RH, Smith MJ: Phylogeny of Pacific salmon and trout based on growth hormone type-2 and mitochondrial NADH dehydrogenase subunit 3 DNA sequences. / Can J Fish Aquatic Sci 1996, 53:1165鈥?176. CrossRef
42. Oleinik AG: On the mutation rates of the mitochondrial and nuclear genomes of salmonid fishes. / Russian Journal of Marine Biology 2000, 26:432鈥?38. CrossRef
43. CHORI - 214 - Children's Hospital Oakland Research Institute - 214 [http://bacpac.chori.org/library.php?id=102]
44. CHORI - 217 - Children's Hospital Oakland Research Institute - 217 [http://bacpac.chori.org/library.php?id=223]
45. CHORI - Children's Hospital Oakland Research Institute [http://bacpac.chori.org/highdensity.htm]
46. Luo M-C, Thomas C, You FM, Hsiao J, Ouyang S, Buell CR, Malandro M, McGuire PE, Anderson OD, Dvorak J: High-throughput fingerprinting of bacterial artificial chromosomes using the SnaPshot labeling kit and sizing of restriction fragments by capillary electrophoresis. / Genomics 2003, 82:378鈥?89. CrossRef
47. Ewing B, Green P: Base-calling of automated sequencer traces using PHRED. II. Error probabilities. / Genome Res 1998, 8:186鈥?94.
48. Ewing B, Hillier L, Wendl MC, Green P: Base-calling of automated sequencer traces using PHRED. I. Accuracy assessment. / Genome Res 1998, 8:175鈥?85.
49. PHRAP [http://bozeman.mbt.washington.edu]
50. Gordon D, Abajan C, Green P: Consed: a graphical tool for sequence finishing. / Genome Res 1998, 8:195鈥?02.
51. Sonnhammer EL, Durbin R: A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis. / Gene 1995, 167:GC1鈥?0. CrossRef
52. Schwartz S, Zhang Z, Frazer KA, Smit A, Riemer C, Bouck J, Gibbs R, Hardison R, Miller W: PipMaker - a web server for aligning two genomic DNA sequences. / Genome Res 2000, 10:577鈥?86. CrossRef
53. Jurka J: Repbase update: a database and an electronic journal of repetitive elements. / Trends Genet 2000, 16:418鈥?20. CrossRef
54. BioEdit [http://www.mbio.ncsu.edu/BioEdit/bioedit.html] - 作者单位：Kristian R von Schalburg (1)
Ryosuke Yazawa (1)
Johan de Boer (1)
Krzysztof P Lubieniecki (2)
Benjamin Goh (3)
Christopher A Straub (1)
Marianne R Beetz-Sargent (1)
Adrienne Robb (1)
William S Davidson (2)
Robert H Devlin (3)
Ben F Koop (1)
1. Centre for Biomedical Research, University of Victoria, Victoria, British Columbia, V8W 3N5, Canada
2. Department of Molecular Biology and Biochemistry, Simon Fraser University, V5A 1S6, Burnaby, British Columbia, Canada
3. Fisheries and Oceans Canada, 4160 Marine Drive, West Vancouver, British Columbia, V7V 1N6, Canada
文摘
Background Growth hormone (GH) is an important regulator of skeletal growth, as well as other adapted processes in salmonids. The GH gene (gh) in salmonids is represented by duplicated, non-allelic isoforms designated as gh1 and gh2. We have isolated and characterized gh-containing bacterial artificial chromosomes (BACs) of both Atlantic and Chinook salmon (Salmo salar and Oncorhynchus tshawytscha) in order to further elucidate our understanding of the conservation and regulation of these loci. Results BACs containing gh1 and gh2 from both Atlantic and Chinook salmon were assembled, annotated, and compared to each other in their coding, intronic, regulatory, and flanking regions. These BACs also contain the genes for skeletal muscle sodium channel oriented in the same direction. The sequences of the genes for interferon alpha-1, myosin alkali light chain and microtubule associated protein Tau were also identified, and found in opposite orientations relative to gh1 and gh2. Viability of each of these genes was examined by PCR. We show that transposon insertions have occurred differently in the promoters of gh, within and between each species. Other differences within the promoters and intronic and 3'-flanking regions of the four gh genes provide evidence that they have distinct regulatory modes and possibly act to function differently and/or during different times of salmonid development. Conclusion A core proximal promoter for transcription of both gh1 and gh2 is conserved between the two species of salmon. Nevertheless, transposon integration and regulatory element differences do exist between the promoters of gh1 and gh2. Additionally, organization of transposon families into the BACs containing gh1 and for the BACs containing gh2, are very similar within orthologous regions, but much less clear conservation is apparent in comparisons between the gh1- and gh2-containing paralogous BACs for the two fish species. This is consistent with the hypothesis that a burst of transposition activity occurred during the speciation events which led to Atlantic and Pacific salmon. The Chinook and other Oncorhynchus GH1s are strikingly different in comparison to the other GHs and this change is not apparent in the surrounding non-coding sequences.