Rising levels of atmospheric oxygen and evolution of Nrf2

Scientific Reports

Volumn 6, Issue , 2016, Pages

  Gacesa, Ranko ^a   Dunlap, Walter C ^a   Barlow, David J ^a   Laskowski, Roman A ^b   Long, Paul F ^c  

^a KING'S COLLEGE LONDON   (United Kingdom)

^b EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

^c KING'S COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

OXYGEN; TRANSCRIPTION FACTOR NRF2;

ANIMAL; ASTRONOMY; ATMOSPHERE; CHEMISTRY; CODON; FUNGUS; GENETICS; MAMMAL; METABOLISM; MOLECULAR EVOLUTION; NUCLEOTIDE SEQUENCE; PHYLOGENY;

ANIMALS; ATMOSPHERE; BASE SEQUENCE; CODON; EARTH (PLANET); EVOLUTION, MOLECULAR; FUNGI; MAMMALS; NF-E2-RELATED FACTOR 2; OXYGEN; PHYLOGENY;

EID: 84974851040     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep27740     Document Type: Article

References (43)

1. Holland, H. D. The oxygenation of The atmosphere and oceans. Philos. Trans. R. Soc. Lond. B. Biol. Sci. 361, 903-15 (2006
2. Schirrmeister, B. E., de Vos, J. M., Antonelli, A., & Bagheri, H. C. Evolution of multicellularity coincided with increased diversification of cyanobacteria and The Great Oxidation Event. Proc. Natl. Acad. Sci. USA 110, 1791-6 (2013
3. Lushchak, V. I. Adaptive response to oxidative stress: Bacteria, fungi, plants and animals. Comp. Biochem. Physiol. C. Toxicol. Pharmacol. 153, 175-90 (2011
4. Sporn, M. B., & Liby, K. T. NRF2 and cancer: The good, The bad and The importance of context. Nat. Rev. Cancer 12, 564-71 (2012
5. Gacesa, R., Dunlap, W. C., & Long, P. F. Bioinformatics analyses provide insight into distant homology of The Keap1-Nrf2 pathway. Free Radic. Biol. Med. 88, 373-380 (2015
6. Caspermeyer, J. New grand tree of life study shows a clock-like trend in The emergence of new species and diversity. Mol. Biol. Evol. 32, 1113-1113 (2015
7. Hedges, S. B., Marin, J., Suleski, M., Paymer, M., & Kumar, S. Tree of life reveals clock-like speciation and diversification. Mol. Biol. Evol. 32, 835-845 (2015
8. Berner, R. A., & Canfield, D. E. A new model for atmospheric oxygen over Phanerozoic time. Am. J. Sci. 289, 333-361 (1989
9. Berner, R
10. Berner, R. A. Phanerozoic atmospheric oxygen: New results using The GEOCARBSULF model. Am. J. Sci. 309, 603-606 (2009
11. Harada, M., Tajika, E., & Sekine, Y. Transition to an oxygen-rich atmosphere with an extensive overshoot triggered by The Paleoproterozoic snowball Earth. Earth Planet. Sci. Lett. 419, 178-186 (2015
12. Lyons, T. W., Reinhard, C. T., & Planavsky, N. J. The rise of oxygen in Earth?s early ocean and atmosphere. Nature 506, 307-15 (2014
13. Sperling, E. A., Halverson, G. P., Knoll, A. H., MacDonald, F. A., & Johnston, D. T. A basin redox transect at The dawn of animal life. Earth Planet. Sci. Lett. 371-372, 143-155 (2013
14. Johnston, D. T., et al. Late Ediacaran redox stability and metazoan evolution. Earth Planet. Sci. Lett. 335-336, 25-35 (2012
15. Anbar, A. D., et al. A whiff of oxygen before The great oxidation event? Science 317, 1903-1906 (2007
16. Kopp, R. E., Kirschvink, J. L., Hilburn, I. a., & Nash, C. Z. The Paleoproterozoic snowball Earth: a climate disaster triggered by The evolution of oxygenic photosynthesis. Proc. Natl. Acad. Sci. USA 102, 11131-11136 (2005
17. Rasmussen, B., Fletcher, I. R., Brocks, J. J., & Kilburn, M. R. Reassessing The first appearance of eukaryotes and cyanobacteria. Nature 455, 1101-1104 (2008
18. Planavsky, N. J., et al. Low mid-proterozoic atmospheric oxygen levels and The delayed rise of animals. Science 346, 635-638 (2014
19. Mills, D. B., & Canfield, D. E. Oxygen and animal evolution: Did a rise of atmospheric oxygen trigger The origin of animals? BioEssays 36, 1145-1155 (2014
20. Zhang, S., et al. Sufficient oxygen for animal respiration 1, 400 million years ago. Proc. Natl. Acad. Sci. 113, 1731-1736 (2016
21. Och, L. M., & Shields-Zhou, G. A. The Neoproterozoic oxygenation event: Environmental perturbations and biogeochemical cycling. Earth-Science Rev. 110, 26-57 (2012
22. Shao, H., Chu, L., Shao, M., Jaleel, C. A., & Mi, H. Higher plant antioxidants and redox signaling under environmental stresses. C. R. Biol. 331, 433-41 (2008
23. Tomitani, A., et al. Chlorophyll b and phycobilins in The common ancestor of cyanobacteria and chloroplasts. Nature 400, 159-162 (1999
24. Nei, M., & Gojobori, T. Simple methods for estimating The numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3, 418-426 (1986
25. Choe, K. P., Leung, C. K., & Miyamoto, M. M. Unique structure and regulation of The nematode detoxification gene regulator, SKN-1: implications to understanding and controlling drug resistance. Drug Metab. Rev. 44, 209-223 (2012
26. An, J. H., et al. Regulation of The Caenorhabditis elegans oxidative stress defense protein SKN-1 by glycogen synthase kinase-3. Proc. Natl. Acad. Sci. USA 102, 16275-80 (2005
27. Sykiotis, G. P., & Bohmann, D. Keap1/Nrf2 signaling regulates oxidative stress tolerance and lifespan in Drosophila. Dev. Cell 14, 76-85 (2008
28. Pitoniak, A., & Bohmann, D. Mechanisms and Functions of Nrf2 Signaling in Drosophila. Free Radic. Biol. Med. 88, 302-313 (2015
29. Blackwell, T. K., Steinbaugh, M. J., Hourihan, J. M., Ewald, C. Y., & Isik, M. SKN-1/Nrf, stress responses, and aging in Caenorhabditis elegans. Free Radic. Biol. Med. 88, 290-301 (2015
30. Aguinaldo, A. M., et al. Evidence for a clade of nematodes, arthropods and other moulting animals. Nature 387, 489-493 (1997
31. Kuhl, M., Cohen, Y., Dalsgaard, T., Jorgensen, B. B., & Revsbech, N. P. Microenvironment and photosynthesis of zooxanthellae in scleractinian corals studied with microsensors for O2, pH and light. Mar. Ecol. Prog. Ser. 117, 159-177 (1995
32. Dunlap, W. C., et al. KEGG orthology-based annotation of The predicted proteome of Acropora digitifera: ZoophyteBase - an open access and searchable database of a coral genome. BMC Genomics 14, 509 (2013
33. Hedges, S. B., Blair, J. E., Venturi, M. L., & Shoe, J. L. A molecular timescale of eukaryote evolution and The rise of complex multicellular life. BMC Evol. Biol. 4, 1-9 (2004
34. Erwin, D. H., et al. The Cambrian conundrum: early divergence and later ecological success in The early history of animals. Science 334, 1091-1097 (2011
35. Luo, Z. X., Yuan, C. X., Meng, Q. J., & Ji, Q. A Jurassic eutherian mammal and divergence of marsupials and placentals. Nature 476, 442-445 (2011
36. Luo, Z., & Martin, T. Analysis of molar structure and phylogeny of docodont genera. Bull. Carnegie Museum Nat. Hist. 39, 27-47 (2007
37. Bouckaert, R., et al. BEAST 2: A Software Platform for Bayesian Evolutionary Analysis. PLoS Comput. Biol. 10, 1-6 (2014
38. Di Tommaso, P., et al. T-Coffee: A web server for The multiple sequence alignment of protein and RNA sequences using structural information and homology extension. Nucleic Acids Res. 39, 1-5 (2011
39. Chang, J.-M., Di Tommaso, P., & Notredame, C. TCS: A new multiple sequence alignment reliability measure to estimate alignment accuracy and improve phylogenetic tree reconstruction. Mol. Biol. Evol. 31, 1625-1637 (2014
40. Wang, D. Y., Kumar, S., & Hedges, S. B. Divergence time estimates for The early history of animal phyla and The origin of plants, animals and fungi. Proc. Biol. Sci. 266, 163-71 (1999
41. Tamura, K., Stecher, G., Peterson, D., Filipski, A., & Kumar, S. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol. Biol. Evol. 30, 2725-9 (2013
42. Larkin, M. A., et al. Clustal W and Clustal X version 2.0. Bioinformatics 23, 2947-2948 (2007
43. Kranendonk, M. J. Van. In Geol. Time Scale 2012 2-Volume Set (Felix, M. G., OggMark James, G., Schmitz, D., & Gab, M. O.) 299-392 (Elsevier, 2012