Modular evolution of PGC-1α in vertebrates

Journal of Molecular Evolution

Volumn 70, Issue 5, 2010, Pages 492-505

  Lemoine, Christophe M R ^a,b   Lougheed, Stephen C ^a   Moyes, Christopher D ^a  

^a QUEEN S UNIVERSITY   (Canada)

^b MCMASTER UNIVERSITY   (Canada)

Author keywords

Coactivator; Genome duplication; MEF; Modularity; Molecular evolution; NRF 1; PPAR; Transcriptional regulation

Indexed keywords

HEAT SHOCK PROTEIN; NUCLEAR RESPIRATORY FACTOR 1; PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR; PPARGC1A PROTEIN, HUMAN; TRANSCRIPTION FACTOR;

AMINO ACID SUBSTITUTION; ANIMAL; ARTICLE; GENETICS; HUMAN; METABOLISM; MOLECULAR EVOLUTION; PHYLOGENY; POINT MUTATION; PROTEIN DATABASE; PROTEIN PROCESSING; SEQUENCE HOMOLOGY; VERTEBRATE;

AMINO ACID SUBSTITUTION; ANIMALS; DATABASES, PROTEIN; EVOLUTION, MOLECULAR; HEAT-SHOCK PROTEINS; HUMANS; NUCLEAR RESPIRATORY FACTOR 1; PEROXISOME PROLIFERATOR-ACTIVATED RECEPTORS; PHYLOGENY; POINT MUTATION; PROTEIN PROCESSING, POST-TRANSLATIONAL; SEQUENCE HOMOLOGY, AMINO ACID; TRANSCRIPTION FACTORS; VERTEBRATES;

MAMMALIA; TELEOSTEI; TETRAPODA; VERTEBRATA;

EID: 77955703525     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-010-9347-x     Document Type: Article

References (77)

1. U Andersson RC Scarpulla 2001 Pgc-1-related coactivator, a novel, serum-inducible coactivator of nuclear respiratory factor 1-dependent transcription in mammalian cells Mol Cell Biol 21 3738 3749 10.1128/MCB.21.11. 3738-3749.2001 1:CAS:528:DC%2BD3MXjs1Oqu7g%3D 11340167 (Pubitemid 32466987)
2. WR Atchley WM Fitch M Bronner-Fraser 1994 Molecular evolution of the MyoD family of transcription factors Proc Natl Acad Sci USA 91 11522 11526 10.1073/pnas.91.24.11522 1:CAS:528:DyaK2MXitlyrsbc%3D 7972095 (Pubitemid 24356376)
3. ML Beçak LS Kobashi 2004 Evolution by polyploidy and gene regulation in Anura Genet Mol Res 3 195 212 15266394
4. MJ Benton PCJ Donoghue 2007 Paleontological evidence to date the tree of life Mol Biol Evol 24 26 53 10.1093/molbev/msl150 1:CAS:528: DC%2BD2sXnvFWgug%3D%3D 17047029 (Pubitemid 46026279)
5. JE Blair SB Hedges 2005 Molecular phylogeny and divergence times of deuterostome animals Mol Biol Evol 22 2275 2284 10.1093/molbev/msi225 1:CAS:528:DC%2BD2MXhtFKjsLvP 16049193 (Pubitemid 41437808)
6. NR Bury A Sturm 2007 Evolution of the corticosteroid receptor signalling pathway in fish Gen Comp Endocrinol 153 47 56 10.1016/j.ygcen.2007.03.009 1:CAS:528:DC%2BD2sXotlShtrc%3D 17470371 (Pubitemid 47103327)
7. W Cao KW Daniel J Robidoux P Puigserver AV Medvedev X Bai LM Floering BM Spiegelman S Collins 2004 p38 mitogen-activated protein kinase is the central regulator of cyclic AMP-dependent transcription of the brown fat uncoupling protein 1 gene Mol Cell Biol 24 3057 3067 10.1128/MCB.24.7.3057-3067.2004 1:CAS:528:DC%2BD2cXis1emt7g%3D 15024092 (Pubitemid 38381292)
8. B Conrad SE Antonarakis 2007 Gene duplication: a drive for phenotypic diversity and cause of human disease Annu Rev Genomics Hum Genet 8 17 35 10.1146/annurev.genom.8.021307.110233 1:CAS:528:DC%2BD2sXht1Wksr3O 17386002
9. AJ Drummond A Rambaut 2007 BEAST: Bayesian evolutionary analysis by sampling trees BMC Evol Biol 7 214 10.1186/1471-2148-7-214 17996036 (Pubitemid 351253125)
10. AJ Drummond SYW Ho MJ Phillips A Rambaut 2006 Relaxed phylogenetics and dating with confidence PLoS Biol 4 e88 10.1371/journal.pbio.0040088 16683862
11. H Escriva V Laudet M Robinson-Rechavi 2003 Nuclear receptors are markers of animal genome evolution J Struct Funct Genomics 3 177 184 10.1023/A:1022638706822 (Pubitemid 36460255)
12. H Escriva S Bertrand V Laudet 2004 The evolution of the nuclear receptor superfamily Essays Biochem 40 11 26 1:CAS:528:DC%2BD2cXlslymsL0%3D 15242336
13. H Escriva S Bertrand P Germain M Robinson-Rechavi M Umbhauer J Cartry M Duffraisse L Holland H Gronemeyer V Laudet 2006 Neofunctionalization in vertebrates: the example of retinoic acid receptors PLoS Genet 2 e102 10.1371/journal.pgen.0020102 16839186 (Pubitemid 44147400)
14. B Gershman O Puig L Hang RM Peitzsch M Tatar RS Garofalo 2007 High-resolution dynamics of the transcriptional response to nutrition in Drosophila: a key role for dFOXO Physiol Genomics 29 24 34 1:CAS:528: DC%2BD2sXktVaru7o%3D 17090700
15. C Handschin BM Spiegelman 2006 Peroxisome proliferator-activated receptor gamma coactivator 1 coactivators, energy homeostasis, and metabolism Endocr Rev 27 728 735 1:CAS:528:DC%2BD2sXns1Wrtw%3D%3D 17018837
16. Hedges SB (2001) Molecular evidence for the early history of living vertebrates. In: Ahlberg PE (ed) Major events in early vertebrate evolution: palaeontology, phylogeny, genetics and development. Taylor and Francis, London, pp 119-134
17. U Hellsten MK Khokha TC Grammer RM Harland P Richardson DS Rokhsar 2007 Accelerated gene evolution and subfunctionalization in the pseudotetraploid frog Xenopus laevis BMC Biol 25 5 31
18. S Hoegg A Meyer 2005 Hox clusters as models for vertebrate genome evolution Trends Genet 21 421 424 10.1016/j.tig.2005.06.004 1:CAS:528: DC%2BD2MXmsVOhtrc%3D 15967537 (Pubitemid 40981787)
19. S Hoegg H Brinkmann JS Taylor A Meyer 2004 Phylogenetic timing of the fish-specific genome duplication correlates with the diversification of teleost fish J Mol Evol 59 190 203 10.1007/s00239-004-2613-z 1:CAS:528: DC%2BD2cXntlCkurg%3D 15486693 (Pubitemid 39128342)
20. N Huang E vom Baur JM Garnier T Lerouge JL Vonesch Y Lutz P Chambon R Losson 1998 Two distinct nuclear receptor interaction domains in NSD1, a novel SET protein that exhibits characteristics of both corepressors and coactivators EMBO J 17 3398 3412 10.1093/emboj/17.12.3398 1:CAS:528:DyaK1cXksFCltLs%3D 9628876 (Pubitemid 28279513)
21. JP Huelsenbeck F Ronquist 2001 MRBAYES: Bayesian inference of phylogeny Bioinformatics 17 754 755 10.1093/bioinformatics/17.8.754 1:STN:280: DC%2BD3MvotV2isw%3D%3D 11524383
22. I Hurley ME Hale VE Prince 2005 Duplication events and the evolution of segmental identity Evol Dev 7 556 567 10.1111/j.1525-142X.2005.05059.x 1:STN:280:DC%2BD2MnmtVWhtQ%3D%3D 16336409 (Pubitemid 41711652)
23. S Jäger C Handschin J St-Pierre BM Spiegelman 2007 AMP-activated protein kinase (AMPK) action in skeletal muscle via direct phosphorylation of PGC-1alpha Proc Natl Acad Sci USA 104 12017 12022 10.1073/pnas.0705070104 17609368 (Pubitemid 47185622)
24. K King-Jones CS Thummel 2005 Nuclear receptors-a perspective from Drosophila Nat Rev Genet 6 311 323 10.1038/nrg1581 1:CAS:528: DC%2BD2MXivFGisrc%3D 15803199 (Pubitemid 40469050)
25. D Kressler SN Schreiber D Knutti A Kralli 2002 The PGC-1-related protein PERC is a selective coactivator of estrogen receptor alpha J Biol Chem 277 13918 13925 10.1074/jbc.M201134200 1:CAS:528:DC%2BD38XjsFWnsbk%3D 11854298 (Pubitemid 34967998)
26. S Kumar SB Hedges 1998 A molecular timescale for vertebrate evolution Nature 392 917 920 10.1038/31927 1:CAS:528:DyaK1cXjtV2jur8%3D 9582070 (Pubitemid 28232061)
27. CMR LeMoine CE Genge CD Moyes 2008 Role of the PGC-1 family in the metabolic adaptation of goldfish to diet and temperature J Exp Biol 211 1448 1455 10.1242/jeb.014951 1:CAS:528:DC%2BD1cXotlCmsbY%3D 18424678 (Pubitemid 351954827)
28. CMR LeMoine PM Craig K Dhekney JJ Kim GB McClelland 2010 Temporal and spatial patterns of gene expression in skeletal muscles in response to swim training in adult zebrafish (Danio rerio) J Comp Physiol B 180 151 160 10.1007/s00360-009-0398-5 1:CAS:528:DC%2BC3cXjtlyguw%3D%3D 19693513
29. J Lin P Puigserver J Donovan P Tarr BM Spiegelman 2002 Peroxisome proliferator-activated receptor gamma coactivator 1beta (PGC-1beta), a novel PGC-1-related transcription coactivator associated with host cell factor J Biol Chem 277 1645 1648 10.1074/jbc.C100631200 1:CAS:528:DC%2BD38XosFejsg%3D%3D 11733490 (Pubitemid 34968733)
30. J Lin H Wu PT Tarr CY Zhang Z Wu O Boss LF Michael P Puigserver E Isotani EN Olson BB Lowell RR Bassel-Duby BM Spiegelman 2002 Transcriptional co-activator PGC-1 alpha drives the formation of slow-twitch muscle fibres Nature 418 797 801 10.1038/nature00904 1:CAS:528:DC%2BD38XmtV2gu7o%3D 12181572
31. HC Lin LZ Holland ND Holland 2006 Expression of the AmphiTcf gene in amphioxus: insights into the evolution of the TCF/LEF gene family during vertebrate evolution Dev Dyn 235 3396 3403 10.1002/dvdy.20971 1:CAS:528:DC%2BD2sXmsVWhsg%3D%3D 17013891 (Pubitemid 44888205)
32. Macqueen DJ, Johnston IA (2008) An update on MyoD evolution in teleosts and a proposed consensus nomenclature to accommodate the tetraploidization of different vertebrate genomes. PLoS ONE 3:e1567
33. GB McClelland PM Craig K Dhekney S Dipardo 2006 Temperature- and exercise-induced gene expression and metabolic enzyme changes in skeletal muscle of adult zebrafish (Danio rerio) J Physiol 577 739 751 10.1113/jphysiol.2006. 119032 1:CAS:528:DC%2BD2sXjslWi 16990399 (Pubitemid 44804024)
34. A Meyer M Schartl 1999 Gene and genome duplications in vertebrates: the one-to-four (-to-eight in fish) rule and the evolution of novel gene functions Curr Opin Cell Biol 11 699 704 10.1016/S0955-0674(99)00039-3 1:CAS:528:DyaK1MXotVKjsb0%3D 10600714
35. A Meyer Y Van de Peer 2005 From 2R to 3R: evidence for a fish-specific genome duplication (FSGD) Bioessays 27 937 945 10.1002/bies.20293 1:CAS:528:DC%2BD2MXhtVKgsb%2FE 16108068 (Pubitemid 41415948)
36. LF Michael Z Wu RB Cheatham P Puigserver G Adelmant JJ Lehman DP Kelly BM Spiegelman 2001 Restoration of insulin-sensitive glucose transporter (GLUT4) gene expression in muscle cells by the transcriptional coactivator PGC-1 Proc Natl Acad Sci USA 98 3820 3825 10.1073/pnas.061035098 1:CAS:528: DC%2BD3MXis1Khsrg%3D 11274399 (Pubitemid 32249855)
37. H Oberkofler E Schraml F Krempler W Patsch 2003 Potentiation of liver X receptor transcriptional activity by peroxisome-proliferator-activated receptor gamma co-activator 1 alpha Biochem J 371 89 96 10.1042/BJ20021665 1:CAS:528:DC%2BD3sXitlCisbo%3D 12470296 (Pubitemid 36458082)
38. Ohno S (1970) Evolution by gene duplication. Springer-Verlag, Berlin, Heidelberg, New York
39. S Ohno 1999 Gene duplication and the uniqueness of vertebrate genomes circa 1970-1999 Semin Cell Dev Biol 10 517 522 10.1006/scdb.1999.0332 1:CAS:528:DyaK1MXnvFOmsb4%3D 10597635 (Pubitemid 129513238)
40. SP Otto J Whitton 2000 Polyploid incidence and evolution Annu Rev Genet 34 401 437 10.1146/annurev.genet.34.1.401 1:CAS:528:DC%2BD3MXlvFOjsg%3D%3D 11092833 (Pubitemid 32065927)
41. G Panopoulou AJ Poustka 2005 Timing and mechanism of ancient vertebrate genome duplications-the adventure of a hypothesis Trends Genet 21 559 567 10.1016/j.tig.2005.08.004 1:CAS:528:DC%2BD2MXhtVWisb3M 16099069 (Pubitemid 41278461)
42. J Parsch CD Meiklejohn E Hauschteck-Jungen P Hunziker DL Hartl 2001 Molecular evolution of the ocnus and janus genes in the Drosophila melanogaster species subgroup Mol Biol Evol 18 801 811 1:CAS:528:DC%2BD3MXjtFykt78%3D 11319264
43. D Posada KA Crandall 1998 MODELTEST: testing the model of DNA substitution Bioinformatics 14 817 818 10.1093/bioinformatics/14.9.817 1:CAS:528:DyaK1MXktlCltw%3D%3D 9918953
44. SJ Prohaska PF Stadler 2004 The duplication of the Hox gene clusters in teleost fishes Theory Biosci 123 89 110 10.1016/j.thbio.2004.03.004 1:CAS:528:DC%2BD2cXnsFyhtb0%3D 18202881 (Pubitemid 38899338)
45. P Puigserver BM Spiegelman 2003 Peroxisome proliferator-activated receptor-gamma coactivator 1 alpha (PGC-1 alpha): transcriptional coactivator and metabolic regulator Endocr Rev 24 78 90 10.1210/er.2002-0012 1:CAS:528:DC%2BD3sXhslOgsbo%3D 12588810 (Pubitemid 36223280)
46. P Puigserver Z Wu CW Park R Graves M Wright BM Spiegelman 1998 A cold-inducible coactivator of nuclear receptors linked to adaptive thermogenesis Cell 92 829 839 10.1016/S0092-8674(00)81410-5 1:CAS:528:DyaK1cXit1Klsb8%3D 9529258 (Pubitemid 28155321)
47. P Puigserver G Adelmant Z Wu M Fan J Xu B O'Malley BM Spiegelman 1999 Activation of PPARgamma coactivator-1 through transcription factor docking Science 286 1368 1371 10.1126/science.286.5443.1368 1:CAS:528:DyaK1MXnsVersrw%3D 10558993 (Pubitemid 29535898)
48. P Puigserver J Rhee J Donovan CJ Walkey JC Yoon F Oriente Y Kitamura J Altomonte H Dong D Accili BM Spiegelman 2003 Insulin-regulated hepatic gluconeogenesis through FOXO1-PGC-1alpha interaction Nature 423 550 555 10.1038/nature01667 1:CAS:528:DC%2BD3sXktVygtbs%3D 12754525 (Pubitemid 36648580)
49. Rambaut A, Drummond AJ (2007) Tracer v1.4. http://beast.bio.ed.ac.uk/ Tracer
50. M Robinson-Rechavi V Laudet 2001 Evolutionary rates of duplicate genes in fish and mammals Mol Biol Evol 18 681 683 1:CAS:528:DC%2BD3MXis1eitrs%3D 11264421
51. JT Rodgers C Lerin W Haas SP Gygi BM Spiegelman P Puigserver 2005 Nutrient control of glucose homeostasis through a complex of PGC-1alpha and SIRT1 Nature 434 113 118 10.1038/nature03354 1:CAS:528:DC%2BD2MXhslClsb0%3D 15744310 (Pubitemid 40349395)
52. F Ronquist JP Huelsenbeck 2003 MRBAYES 3: Bayesian phylogenetic inference under mixed models Bioinformatics 19 1572 1574 10.1093/bioinformatics/btg180 1:CAS:528:DC%2BD3sXntlKms7k%3D 12912839 (Pubitemid 37038874)
53. Ronquist F, Huelsenbeck JP, van der Mark P (2005) MrBayes 3.1 Manual. Published online at: http://mrbayes.csit.fsu.edu/manual.php
54. P Sadana EA Park 2007 Characterization of the transactivation domain in the peroxisome-proliferator-activated receptor gamma co-activator (PGC-1) Biochem J 403 511 518 10.1042/BJ20061526 1:CAS:528:DC%2BD2sXltVejsL8%3D 17284167 (Pubitemid 46706979)
55. RC Scarpulla 2006 Nuclear control of respiratory gene expression in mammalian cells J Cell Biochem 97 673 683 10.1002/jcb.20743 1:CAS:528: DC%2BD28Xis1Crs7s%3D 16329141
56. RC Scarpulla 2008 Transcriptional paradigms in mammalian mitochondrial biogenesis and function Physiol Rev 88 611 638 10.1152/physrev.00025.2007 1:CAS:528:DC%2BD1cXls1KhsLw%3D 18391175 (Pubitemid 351520089)
57. M Sémon KH Wolfe 2007 Consequences of genome duplication Curr Opin Genet Dev 17 505 512 10.1016/j.gde.2007.09.007 18006297 (Pubitemid 350186344)
58. Steinke D, Hoegg S, Brinkmann H, Meyer A (2006) Three rounds (1R/2R/3R) of genome duplications and the evolution of the glycolytic pathway in vertebrates. BMC Biol 4:16
59. Swofford DL, PAUP*(2000) Phylogenetic analysis using parsimony (*and other methods). Version 4. Sinauer Associates, Sunderland, Massachusetts
60. K Tamura J Dudley M Nei S Kumar 2007 MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0 Mol Biol Evol 24 1596 1599 10.1093/molbev/msm092 1:CAS:528:DC%2BD2sXpsVGrsL8%3D 17488738 (Pubitemid 47236692)
61. JS Taylor I Braasch T Frickey A Meyer Y Van de Peer 2003 Genome duplication, a trait shared by 22000 species of ray-finned fish Genome Res 13 382 390 10.1101/gr.640303 1:CAS:528:DC%2BD3sXit1Wgtrc%3D 12618368 (Pubitemid 36395395)
62. C Teyssier H Ma R Emter A Kralli MR Stallcup 2005 Activation of nuclear receptor coactivator PGC-1alpha by arginine methylation Genes Dev 19 1466 1473 10.1101/gad.1295005 1:CAS:528:DC%2BD2MXlslChu70%3D 15964996 (Pubitemid 41003013)
63. JD Thompson DG Higgins TJ Gibson 1994 CLUSTAL W: improving the sensitivity of progressive multiple sequence alignments through sequence weighting, position specific gap penalties and weight matrix choice Nucleic Acids Res 22 4673 4680 10.1093/nar/22.22.4673 1:CAS:528:DyaK2MXitlSgu74%3D 7984417
64. M Ueda K Watanabe K Sato Y Akiba M Toyomizu 2005 Possible role for avPGC-1alpha in the control of expression of fiber type, along with avUCP and avANT mRNAs in the skeletal muscles of cold-exposed chickens FEBS Lett 579 11 17 10.1016/j.febslet.2004.11.039 1:CAS:528:DC%2BD2cXhtFGht7rM 15620684 (Pubitemid 40023367)
65. M Uldry W Yang J St-Pierre J Lin P Seale BM Spiegelman 2006 Complementary action of the PGC-1 coactivators in mitochondrial biogenesis and brown fat differentiation Cell Metab 3 333 341 10.1016/j.cmet.2006.04.002 1:CAS:528:DC%2BD28XltF2isLs%3D 16679291
66. RB Vega JM Huss DP Kelly 2000 The coactivator PGC-1 cooperates with peroxisome proliferator-activated receptor alpha in transcriptional control of nuclear genes encoding mitochondrial fatty acid oxidation enzymes Mol Cell Biol 20 1868 1876 10.1128/MCB.20.5.1868-1876.2000 1:CAS:528:DC%2BD3cXhtF2ntb8%3D 10669761 (Pubitemid 30100203)
67. B Venkatesh 2003 Evolution and diversity of fish genomes Curr Opin Genet Dev 13 588 592 10.1016/j.gde.2003.09.001 1:CAS:528:DC%2BD3sXpt1SnsLg%3D 14638319 (Pubitemid 37456876)
68. K Vercauteren RA Pasko N Gleyzer VM Marino RC Scarpulla 2006 PGC-1-related coactivator: immediate early expression and characterization of a CREB/NRF-1 binding domain associated with cytochrome c promoter occupancy and respiratory growth Mol Cell Biol 26 7409 7419 10.1128/MCB.00585-06 1:CAS:528:DC%2BD28XhtFCgurzK 16908542 (Pubitemid 44547693)
69. K Vercauteren N Gleyzer SC Scarpulla 2008 PGC-1-related coactivator complexes with HCF-1 and NRF-2beta in mediating NRF-2(GABP)-dependent respiratory gene expression J Biol Chem 283 12102 12111 10.1074/jbc.M710150200 1:CAS:528:DC%2BD1cXltVyrsbo%3D 18343819
70. GP Wagner C Fried SJ Prohaska PF Stadler 2004 Divergence of conserved non-coding sequences: rate estimates and relative rate tests Mol Biol Evol 21 2116 2121 10.1093/molbev/msh221 1:CAS:528:DC%2BD2cXptVKns7c%3D 15282332 (Pubitemid 39391988)
71. A Woolfe G Elgar 2007 Comparative genomics using Fugu reveals insights into regulatory subfunctionalization Genome Biol 8 R53 10.1186/gb-2007-8-4-r53 17428329 (Pubitemid 351859209)
72. Z Wu P Puigserver U Andersson C Zhang G Adelmant V Mootha A Troy S Cinti B Lowell RC Scarpulla BM Spiegelman 1999 Mechanisms controlling mitochondrial biogenesis and respiration through the thermogenic coactivator PGC-1 Cell 98 115 124 10.1016/S0092-8674(00)80611-X 1:CAS:528:DyaK1MXks1Kktrs%3D 10412986 (Pubitemid 29331201)
73. Y Wu P Delerive WW Chin TP Burris 2002 Requirement of helix 1 and the AF-2 domain of the thyroid hormone receptor for coactivation by PGC-1 J Biol Chem 277 8898 8905 10.1074/jbc.M110761200 1:CAS:528:DC%2BD38Xitl2ltbc%3D 11751919 (Pubitemid 34952959)
74. Z Yang 1997 PAML: a program package for phylogenetic analysis by maximum likelihood Comput Appl BioSci 13 555 556 1:CAS:528:DyaK2sXntlGnu7s%3D 9367129
75. J Zhang 2003 Evolution by gene duplication: an update Trends Ecol Evol 18 292 298 10.1016/S0169-5347(03)00033-8 (Pubitemid 36631749)
76. SL Zhang WS Lu L Yan MC Wu MT Xu LH Chen H Cheng 2007 Association between peroxisome proliferator-activated receptor-gamma coactivator-1alpha gene polymorphisms and type 2 diabetes in southern Chinese population: role of altered interaction with myocyte enhancer factor 2C Chin Med J 120 1878 1885 1:CAS:528:DC%2BD2sXhsVGgtb3O 18067759
77. ZD Zhang P Cayting G Weinstock M Gerstein 2008 Analysis of nuclear receptor pseudogenes in vertebrates: how the silent tell their stories Mol Biol Evol 25 131 143 10.1093/molbev/msm251 18065488