Ancient atmospheres and the evolution of oxygen sensing via the hypoxia-inducible factor in metazoans

Physiology

Volumn 25, Issue 5, 2010, Pages 272-279

  Taylor, Cormac T ^a   McElwain, Jennifer C ^a  

^a UNIVERSITY COLLEGE DUBLIN   (Ireland)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 77958042201     PISSN: 15489213     EISSN: 15489221     Source Type: Journal    
DOI: 10.1152/physiol.00029.2010     Document Type: Review

References (67)

1. 2. Proc Natl Acad Sci USA 102:1302-1305, 2005.
2. 2 event on the terrestrial carbon cycle. Proc Natl Acad Sci USA 97:12428-12432, 2000.
3. 2 decline in the late Palaeozoic era. Nature 410:352-354, 2001.
4. 2 redefine paleoatmospheric predictions for the Mesozoic. Science 321:1197-1200, 2008.
5. Benton M, Donoghue PCJ, Asher RJ. Calibrating and constraining molecular clocks. In: The Timetree of Life, edited by Hedges SB, Kumar S. Oxford, UK: Oxford Univ. Press, 2009, p. 89-98.
6. Bergman NM, Lenton TM, Watson AJ. COPSE: a new model of biogeochemical cycling over phanerozoic time. Am J Sci 304:397-437, 2004.
7. 2. Geochimica 70:5653-5664, 2006.
8. Berner RA, Beerling DJ, Dudley R, Robinson JM, Wildman RA Jr. Phanerozoic atmospheric oxygen. Annu Rev Earth Planet Sci 31:105, 2003.
9. Berner RA, Vandenbrooks JM, Ward PD. Evolution. Oxygen and evolution. Science 316:557-558, 2007.
10. Berner RA. Atmospheric oxygen over Phanerozoic time. Proc Natl Acad Sci USA 96:10955-10957, 1999.
11. 2. Oxford, UK: Oxford Univ. Press, 2004.
12. Berner RA. Phanerozoic atmospheric oxygen: new results using the geocarbsulf model. Am J Sci 309:603-606, 2009.
13. Bishop T, Lau KW, Epstein AC, Kim SK, Jiang M, O'Rourke D, Pugh CW, Gleadle JM, Taylor MS, Hodgkin J, Ratcliffe PJ. Genetic analysis of pathways regulated by the von Hippel-Lindau tumor suppressor in Caenorhabditis elegans. PLoS Biol 2:e289, 2004.
14. Bordoli L, Netsch M, Luthi U, Lutz W, Eckner R. Plant orthologs of p300/CBP: conservation of a core domain in metazoan p300/CBP acetyltransferase-related proteins. Nucleic Acids Res 29:589-597, 2001.
15. Budd GE. The earliest fossil record of the animals and its significance. Philos Trans R Soc Lond B Biol Sci 363:1425-1434, 2008.
16. Cao YB, Chen XQ, Wang S, Wang YX, Du JZ. Evolution and regulation of the downstream gene of hypoxia-inducible factor-1alpha in naked carp (Gymnocypris przewalskii) from lake Qinghai, China. J Mol Evol 67:570-580. 2008.
17. Colgan SP, Taylor CT. Hypoxia: an alarm signal during intestinal inflammation. Nat Rev Gastroenterol Hepatol 7:281-287, 2010.
18. Conway MS. Darwin's dilemma: the realities of the Cambrian 'explosion'. Philos Trans R Soc Lond B Biol Sci 361:1069-1083, 2006.
19. Cramer T, Yamanishi Y, Clausen BE, Förster I, Pawlinski R, Mackman N, Haase VH, Jaenisch R, Corr M, Nizet V, Firestein GS, Gerber HP, Ferrara N, Johnson RS. HIF-1alpha is essential for myeloid cell-mediated inflammation. Cell 112:645-657, 2003.
20. Dole M. The natural history of oxygen. J Gen Physiol 49:5-27, 1965.
21. Dudley R. Atmospheric oxygen, giant Paleozoic insects and the evolution of aerial locomotor performance. J Exp Biol 201:1043-1050, 1998.
22. Epstein AC, Gleadle JM, McNeill LA, Hewitson KS, O'Rourke J, Mole DR, Mukherji M, Metzen E, Wilson MI, Dhanda A, Tian YM, Masson N, Hamilton DL, Jaakkola P, Barstead R, Hodgkin J, Maxwell PH, Pugh CW, Schofield CJ, Ratcliffe PJ. C. elegans EGL-9 and mammalian homologs define a family of dioxygenases that regulate HIF by prolyl hydroxylation. Cell 107:43-54, 2001.
23. Falkowski PG, Katz ME, Milligan AJ, Fennel K, Cramer BS, Aubry MP, Berner RA, Novacek MJ, Zapol WM. The rise of oxygen over the past 205 million years and the evolution of large placental mammals. Science 309:2202-2204, 2005.
24. Fraisl P, Aragonés J, Carmeliet P. Inhibition of oxygen sensors as a therapeutic strategy for ischaemic and inflammatory disease. Nat Rev Drug Discov 8:139-152, 2009.
25. Frazier MR, Woods HA, Harrison JF. Interactive effects of rearing temperature and oxygen on the development of Drosophila melanogaster. Physiol Biochem Zool 74:641-650, 2001.
26. Hagen T, Taylor CT, Lam F, Moncada S. Redistribution of intracellular oxygen in hypoxia by nitric oxide: effect on HIF1alpha. Science 302:1975-1978, 2003.
27. Hampton-Smith RJ, Peet DJ. From polyps to people: a highly familiar response to hypoxia. Ann NY Acad Sci 1177:19-29, 2009.
28. Hedges Life SB. The Timetree of Life, edited by Hedges SB, Kumar S. Oxford, UK: Oxford Univ. Press, 2009, p. 89-98.
29. Higgins DF, Kimura K, Bernhardt WM, Shrimanker N, Akai Y, Hohenstein B, Saito Y, Johnson RS, Kretzler M, Cohen CD, Eckardt KU, Iwano M, Haase VH. Hypoxia promotes fibrogenesis in vivo via HIF-1 stimulation of epithelial-to-mesenchymal transition. J Clin Invest 117:3810-3820, 2007.
30. 2 concentrations in the atmosphere. Photosynth Res 87:177-194, 2006.
31. Imaoka S, Muraguchi T, Kinoshita T. Isolation of xenopus HIF-prolyl 4-hydroxylase and rescue of a small-eye phenotype caused by Siah2 overex-pression. Biochem Biophys Res Commun 355:419-425, 2007.
32. Iyer NV, Leung SW, Semenza GL. The human hypoxia-inducible factor 1alpha gene: HIF1A structure and evolutionary conservation. Genomics 52:159-165, 1998.
33. Kaelin WG Jr, Ratcliffe PJ. Oxygen sensing by metazoans: the central role of the HIF hydroxylase pathway. Mol Cell 30:393-402, 2008.
34. Latif F, Tory K, Gnarra J, Yao M, Duh FM, Orcutt ML, Stackhouse T, Kuzmin I, Modi W, Geil L, Schmidt L, et al. Identification of the von Hippel-Lindau disease tumor suppressor gene. Science 260:1317-1320, 1993. (Pubitemid 23231974)
35. Leite RB, Brito AB, Cancela ML. An oxygen molecular sensor, the HIF prolyl 4-hydroxylase, in the marine protist Perkinsus olseni. Protist 159:355-368, 2008.
36. Lieb ME, Menzies K, Moschella MC, Ni R, Taubman MB. Mammalian EGLN genes have distinct patterns of mRNA expression and regulation. Biochem Cell Biol 80:421-426, 2002.
37. Mahon PC, Hirota K, Semenza GL. FIH-1: a novel protein that interacts with HIF-1alpha and VHL to mediate repression of HIF-1 transcriptional activity. Genes Dev 15:2675-2686, 2001.
38. Margulis L, Bermudes D. Symbiosis as a mechanism of evolution: status of cell symbiosis theory. Symbiosis 1:101-124, 1985.
39. Mason SD, Rundqvist H, Papandreou I, Duh R, McNulty WJ, Howlett RA, Olfert IM, Sundberg CJ, Denko NC, Poellinger L, Johnson RS. HIF-1alpha in endurance training: suppression of oxidative metabolism. Am J Physiol Regul Integr Comp Physiol 293:R2059-R2069, 2007.
40. McElwain JC, Wagner PJ, Hesselbo SP. Science Fossil plant relative abundances indicate sudden loss of late Triassic biodiversity in East Green-land. Science 324:1554-1556, 2009.
41. McElwain JC, Willis KJ, Niklas K. Long term fluctuations in atmospheric carbon dioxide concentration influence plant speciation rate. In: Climate Change and Systematics, edited by Hodkinson T, Jones M, Parnell J, Waldren S. Cambridge, MA: Cambridge Univ. Press, 2010.
42. Nikinmaa M, Rees BB. Oxygen-dependent gene expression in fishes. Am J Physiol Regul Integr Comp Physiol 288:R1079-R1090, 2005.
43. Nisbett EG, Sleep NH. The habit and nature of early life. Nature 409:1083-1091, 2001.
44. Oliver KM, Taylor CT, Cummins Hypoxia EP. Regulation of NFkappaB signalling during inflammation: the role of hydroxylases. Arthritis Res Ther 11:215, 2009.
45. 2 decline over the past 24 million years. Nature 460:85-88, 2009.
46. Powell-Coffman JA, Bradfield CA, Wood WB. Caenorhabditis elegans orthologs of the aryl hydrocarbon receptor and its heterodimerization partner the aryl hydrocarbon receptor nuclear translocator. Proc Natl Acad Sci USA 95:2844-2849, 1998.
47. Powell-Coffman JA. Hypoxia signaling and resistance in C. elegans. Trends Endocrinol Metab 21:435-440, 2010.
48. Ratcliffe PJ, O'Rourke JF, Maxwell PH, Pugh CW. Oxygen sensing, hypoxia-inducible factor-1 and the regulation of mammalian gene expression. J Exp Biol 201:1153-1162, 1998.
49. Retallack GJ. A 300-million year record of atmospheric carbon dioxide from fossil plant cuticles. Nature 411:287-290, 2001.
50. Rich PR. The molecular machinery of Keilin's respiratory chain. Biochem Soc Trans 31:1095-1105, 2003.
51. Rojas DA, Perez-Munizaga DA, Centanin L, Antonelli M, Wappner P, Allende ML, Reyes AE. Cloning of HIF-1a and HIF-2a and mRNA expression pattern during development in zebrafish. Gene Expr Patterns 7:399-345, 2007.
52. Rytkönen KT, Ryyns̈nen HJ, Nikinmaa M, Primmer CR. Variable patterns in the molecular evolution of the hypoxia-inducible factor-1 alpha (HIF-1alpha) gene in teleost fishes and mammals. Gene 420:1-10, 2008.
53. Semenza GL. Life with oxygen. Science 318:62-64, 2007.
54. Semenza GL, Wang GL. A nuclear factor induced by hypoxia via de novo protein synthesis binds to the human erythropoietin gene enhancer at a site required for transcriptional activation. Mol Cell Biol 12:5447-5454, 1992.
55. Sikora S, Godzik A. Combination of multiple alignment analysis and surface mapping paves a way for a detailed pathway reconstruction - The case of VHL (von Hipple Lindau) protein and angiogenesis regulatory pathway. Protein Sci 13:786-796, 2004.
56. Simonson TS, Yang Y, Huff CD, Yun H, Qin G, Witherspoon DJ, Bai Z, Lorenzo FR, Xing J, Jorde LB, Prchal JT, Ge R. Genetic evidence for high-altitude adaptation in Tibet. Science 329:72-75, 2010.
57. Takeda N, O'Dea EL, Doedens A, Kim JW, Weidemann A, Stockmann C, Asagiri M, Simon MC, Hoffmann A, Johnson RS. Differential activation and antagonistic function of HIF-alpha isoforms in macrophages are essential for NO homeostasis. Genes Dev 24:491-501, 2010.
58. Taylor CT, Cummins EP. Hypoxia-responsive transcription factors. Pflügers Arch 450:363-371, 2005.
59. Taylor CT, Pouyssegur J. Oxygen, hypoxia, stress. Ann NY Acad Sci 1113:87-94, 2007.
60. Taylor CT. Interdependent roles for hypoxia inducible factor and nuclear factor-kappaB in hypoxic inflammation. J Physiol 586:4055-4059, 2008.
61. Taylor CT. Mitochondria and cellular oxygen sensing in the HIF pathway. Biochem J 409:19-26, 2008.
62. Ward P, Labandeira C, Laurin M, Berner RA. Confirmation of Romer's Gap as a low oxygen interval constraining the timing of initial arthropod and vertebrate terrestrialization. Proc Natl Acad Sci USA 103:16818-16822, 2006.
63. Weidemann A, Johnson RS. Biology of HIF1alpha. Cell Death Differ 15:621-627, 2008.
64. Woodward ER, Buchberger A, Clifford SC, Hurst LD, Affara NA, Maher ER. Comparative sequence analysis of the VHL tumor suppressor gene. Genomics 65:253-265, 2000.
65. Zelzer E, Wappner P, Shilo BZ. The PAS domain confers target gene specificity of Drosophila bHLH/PAS proteins. Genes Dev 11:2079-2089, 1997.
66. Zhang N, Fu Z, Linke S, Chicher J, Gorman JJ, Visk D, Haddad GG, Poellinger L, Peet DJ, Powell F, Johnson RS. The asparaginyl hydroxylase factor inhibiting HIF-1alpha is an essential regulator of metabolism. Cell Metab 11:364-378, 2010.
67. Zhou D, Visk DW, Haddad GG. Drosophila, a golden bug, for the dissection of the genetic basis of tolerance and susceptibility to hypoxia. Pediatr Res 66:239-247.