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Mechanisms for the Evolution of a Derived Function in the Ancestral Glucocorticoid Receptor


Understanding the genetic, structural, and biophysical mechanisms that caused protein functions to evolve is a central goal of molecular evolutionary studies. Ancestral sequence reconstruction (ASR) offers an experimental approach to these questions. Here we use ASR to shed light on the earliest functions and evolution of the glucocorticoid receptor (GR), a steroid-activated transcription factor that plays a key role in the regulation of vertebrate physiology. Prior work showed that GR and its paralog, the mineralocorticoid receptor (MR), duplicated from a common ancestor roughly 450 million years ago; the ancestral functions were largely conserved in the MR lineage, but the functions of GRs—reduced sensitivity to all hormones and increased selectivity for glucocorticoids—are derived. Although the mechanisms for the evolution of glucocorticoid specificity have been identified, how reduced sensitivity evolved has not yet been studied. Here we report on the reconstruction of the deepest ancestor in the GR lineage (AncGR1) and demonstrate that GR's reduced sensitivity evolved before the acquisition of restricted hormone specificity, shortly after the GR–MR split. Using site-directed mutagenesis, X-ray crystallography, and computational analyses of protein stability to recapitulate and determine the effects of historical mutations, we show that AncGR1's reduced ligand sensitivity evolved primarily due to three key substitutions. Two large-effect mutations weakened hydrogen bonds and van der Waals interactions within the ancestral protein, reducing its stability. The degenerative effect of these two mutations is extremely strong, but a third permissive substitution, which has no apparent effect on function in the ancestral background and is likely to have occurred first, buffered the effects of the destabilizing mutations. Taken together, our results highlight the potentially creative role of substitutions that partially degrade protein structure and function and reinforce the importance of permissive mutations in protein evolution.


Vyšlo v časopise: Mechanisms for the Evolution of a Derived Function in the Ancestral Glucocorticoid Receptor. PLoS Genet 7(6): e32767. doi:10.1371/journal.pgen.1002117
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1002117

Souhrn

Understanding the genetic, structural, and biophysical mechanisms that caused protein functions to evolve is a central goal of molecular evolutionary studies. Ancestral sequence reconstruction (ASR) offers an experimental approach to these questions. Here we use ASR to shed light on the earliest functions and evolution of the glucocorticoid receptor (GR), a steroid-activated transcription factor that plays a key role in the regulation of vertebrate physiology. Prior work showed that GR and its paralog, the mineralocorticoid receptor (MR), duplicated from a common ancestor roughly 450 million years ago; the ancestral functions were largely conserved in the MR lineage, but the functions of GRs—reduced sensitivity to all hormones and increased selectivity for glucocorticoids—are derived. Although the mechanisms for the evolution of glucocorticoid specificity have been identified, how reduced sensitivity evolved has not yet been studied. Here we report on the reconstruction of the deepest ancestor in the GR lineage (AncGR1) and demonstrate that GR's reduced sensitivity evolved before the acquisition of restricted hormone specificity, shortly after the GR–MR split. Using site-directed mutagenesis, X-ray crystallography, and computational analyses of protein stability to recapitulate and determine the effects of historical mutations, we show that AncGR1's reduced ligand sensitivity evolved primarily due to three key substitutions. Two large-effect mutations weakened hydrogen bonds and van der Waals interactions within the ancestral protein, reducing its stability. The degenerative effect of these two mutations is extremely strong, but a third permissive substitution, which has no apparent effect on function in the ancestral background and is likely to have occurred first, buffered the effects of the destabilizing mutations. Taken together, our results highlight the potentially creative role of substitutions that partially degrade protein structure and function and reinforce the importance of permissive mutations in protein evolution.


Zdroje

1. AnfinsenCB 1959 The molecular basis of evolution. New York Wiley

2. PaulingLZuckerkandlE 1963 Chemical paleogenetics: molecular "restoration studies" of extinct forms of life. Acta Chem Scand 17 S9 S16

3. OhnoS 1970 Evolution by gene duplication. BerlinNew York Springer-Verlag

4. KimuraM 1974 Gene pool of higher organisms as a product of evolution. Cold Spring Harb Symp Quant Biol 38 515 524

5. PerutzMF 1983 Species adaptation in a protein molecule. Mol Biol Evol 1 1 28

6. GoldingGBDeanAM 1998 The structural basis of molecular adaptation. Mol Biol Evol 15 355 369

7. ZuckerkandlEPaulingL 1965 Molecules as documents of evolutionary history. J Theor Biol 8 357 366

8. SerranoLDayAGFershtAR 1993 Step-wise mutation of barnase to binase. A procedure for engineering increased stability of proteins and an experimental analysis of the evolution of protein stability. J Mol Biol 233 305 312

9. CapraJASinghM 2008 Characterization and prediction of residues determining protein functional specificity. Bioinformatics 24 1473 1480

10. DonaldJEShakhnovichEI 2009 SDR: a database of predicted specificity-determining residues in proteins. Nucleic Acids Res 37 D191 4

11. GerltJABabbittPC 2009 Enzyme (re)design: lessons from natural evolution and computation. Curr Opin Chem Biol 13 10 18

12. HarmsMJThorntonJW 2010 Analyzing protein structure and function using ancestral gene reconstruction. Curr Opin Struct Biol 20 360 366

13. BloomJDSilbergJJWilkeCDrummondDAAdamiC 2005 Thermodynamic prediction of protein neutrality. P Natl Acad Sci USA 102 606 611

14. BershteinSSegalMBekermanRTokurikiNTawfikDS 2006 Robustness-epistasis link shapes the fitness landscape of a randomly drifting protein. Nature 444 929 932

15. OrtlundEABridghamJTRedinboMRThorntonJW 2007 Crystal structure of an ancient protein: Evolution by conformational epistasis. Science 317 1544 1548

16. BridghamJTOrtlundEAThorntonJW 2009 An epistatic ratchet constrains the direction of glucocorticoid receptor evolution. Nature 461 515 519

17. TomatisPEFabianeSMSimonaFCarloniPSuttonBJ 2008 Adaptive protein evolution grants organismal fitness by improving catalysis and flexibility. Proc Natl Acad Sci U S A 105 20605 20610

18. ThorntonJW 2004 Resurrecting ancient genes: experimental analysis of extinct molecules. Nat Rev Genet 5 366 375

19. BridghamJTCarrollSMThorntonJW 2006 Evolution of hormone-receptor complexity by molecular exploitation. Science 312 97 101

20. BeatoM 1989 Gene regulation by steroid hormones. Cell 56 335 344

21. BentleyPJ 1998 Comparative vertebrate endocrinology. New York Cambridge University Press

22. ArrizaJLWeinbergerCCerelliGGlaserTMHandelinBL 1987 Cloning of human mineralocorticoid receptor complementary DNA: structural and functional kinship with the glucocorticoid receptor. Science 237 268 275

23. CarrollSMBridghamJTThorntonJW 2008 Evolution of hormone signaling in elasmobranchs by exploitation of promiscuous receptors. Mol Biol Evol 25 2643 2652

24. ThorntonJW 2001 Evolution of vertebrate steroid receptors from an ancestral estrogen receptor by ligand exploitation and serial genome expansions. Proc Natl Acad Sci U S A 98 5671 5676

25. GelsleichterJMusickJA 1999 Effects of insulin-like growth factor-I, corticosterone, and 3,3′, 5-tri-iodo-L-thyronine on glycosaminoglycan synthesis in vertebral cartilage of the clearnose skate, Raja eglanteria. J Exp Zool 284 549 556

26. NunezBSEvansANSimpsonMAWongWPIpYK 2006 Characterization of cDNAs encoding cholesterol side chain cleavage and 3beta-hydroxysteroid dehydrogenase in the freshwater stingray Potamotrygon motoro. Comp Biochem Physiol B Biochem Mol Biol 145 306 317

27. NunezSTrantJM 1999 Regulation of interrenal gland steroidogenesis in the Atlantic stingray (Dasyatis sabina). J Exp Zool 284 517 525

28. ManireCARasmussenLELMaruskaKPTricasTC 2007 Sex, seasonal, and stress-related variations in elasmobranch corticosterone concentrations. Comp Biochem Phys A 148 926 935

29. HazonNHendersonIW 1984 Secretory dynamics of 1 alpha-hydroxycorticosterone in the elasmobranch fish, Scyliorhinus canicula. J Endocrinol 103 205 211

30. ArmourKJO'TooleLBHazonN 1993 The effect of dietary protein restriction on the secretory dynamics of 1 alpha-hydroxycorticosterone and urea in the dogfish, Scyliorhinus canicula: a possible role for 1 alpha-hydroxycorticosterone in sodium retention. J Endocrinol 138 275 282

31. HillisDM 1998 Taxonomic sampling, phylogenetic accuracy, and investigator bias. Syst Biol 47 3 8

32. HeathTAZwicklDJKimJHillisDM 2008 Taxon sampling affects inferences of macroevolutionary processes from phylogenetic trees. Syst Biol 57 160 166

33. PollockDDZwicklDJMcGuireJAHillisDM 2002 Increased taxon sampling is advantageous for phylogenetic inference. Syst Biol 51 664 671

34. IdlerDRTruscottB 1966 1-alpha-hydroxycorticosterone from cartilaginous fish: a new adrenal steroid in blood. Journal of the Fisheries Research Board of Canada 23 615 619

35. TruscottBIdlerDR 1972 Corticosteroids in plasma of elasmobranchs. Comp Biochem Physiol A 42 41 50

36. Hanson-SmithVKolaczkowskiBThorntonJW 2010 Robustness of ancestral sequence reconstruction to phylogenetic uncertainty. Mol Biol Evol 27 1988 1999

37. BledsoeRKMontanaVGStanleyTBDelvesCJApolitoCJ 2002 Crystal structure of the glucocorticoid receptor ligand binding domain reveals a novel mode of receptor dimerization and coactivator recognition. Cell 110 93 105

38. NagyLSchwabeJW 2004 Mechanism of the nuclear receptor molecular switch. Trends Biochem Sci 29 317 324

39. FengWRibeiroRCWagnerRLNguyenHAprilettiJW 1998 Hormone-dependent coactivator binding to a hydrophobic cleft on nuclear receptors. Science 280 1747 1749

40. KauppiBJakobCFarnegardhMYangJAholaH 2003 The three-dimensional structures of antagonistic and agonistic forms of the glucocorticoid receptor ligand-binding domain: RU-486 induces a transconformation that leads to active antagonism. J Biol Chem 278 22748 22754

41. BledsoeRKMadaussKPHoltJAApolitoCJLambertMH 2005 A ligand-mediated hydrogen bond network required for the activation of the mineralocorticoid receptor. J Biol Chem 280 31283 31293

42. LiYSuinoKDaughertyJXuHE 2005 Structural and biochemical mechanisms for the specificity of hormone binding and coactivator assembly by mineralocorticoid receptor. Mol Cell 19 367 380

43. SchymkowitzJBorgJStricherFNysRRousseauF 2005 The FoldX web server: an online force field. Nucleic Acids Res 33 W382 8

44. MatthewsBW 1987 Genetic and structural analysis of the protein stability problem. Biochemistry 26 6885 6888

45. MatthewsBW 1993 Structural and genetic analysis of protein stability. Annu Rev Biochem 62 139 160

46. TokurikiNStricherFSchymkowitzJSerranoLTawfikDS 2007 The stability effects of protein mutations appear to be universally distributed. Journal of molecular biology 369 1318 1332

47. BloomJDArnoldFHWilkeC 2007 Breaking proteins with mutations: threads and thresholds in evolution. Mol Syst Biol 3 1 2

48. BloomJDArnoldF 2009 In the Light of Evolution III: Two Centuries of Darwin Sackler Colloquium: In the light of directed evolution: Pathways of adaptive protein evolution. Proc Natl Acad Sci U S A 106 9995 10000

49. BloomJDLabthavikulSTOteyCRArnoldFH 2006 Protein stability promotes evolvability. Proc Natl Acad Sci U S A 103 5869 5874

50. TokurikiNTawfikDS 2009 Chaperonin overexpression promotes genetic variation and enzyme evolution. Nature 459 668 673

51. BershteinSTawfikDS 2008 Advances in laboratory evolution of enzymes. Current opinion in chemical biology 12 151 158

52. MitrakiAFaneBHaase-PettingellCSturtevantJKingJ 1991 Global suppression of protein folding defects and inclusion body formation. Science 253 54 58

53. ShortleDLinB 1985 Genetic analysis of staphylococcal nuclease: identification of three intragenic "global" suppressors of nuclease-minus mutations. Genetics 110 539 555

54. BershteinSGoldinKTawfikDS 2008 Intense neutral drifts yield robust and evolvable consensus proteins. Journal of Molecular Biology 379 1029 1044

55. TokurikiNStricherFSerranoLTawfikDS 2008 How protein stability and new functions trade off. PLoS Comput Biol 4 e1000002 doi:10.1371/journal.pcbi.1000002

56. FieldSFMatzMV 2010 Retracing evolution of red fluorescence in GFP-like proteins from Faviina corals. Mol Biol Evol 27 225 233

57. DrummondDABloomJDAdamiCWilkeCOArnoldFH 2005 Why highly expressed proteins evolve slowly. Proc Natl Acad Sci U S A 102 14338 14343

58. BloomJDGongLIBaltimoreD 2010 Permissive secondary mutations enable the evolution of influenza oseltamivir resistance. Science 328 1272 1275

59. GarabedianMJYamamotoKR 1992 Genetic dissection of the signaling domain of a mammalian steroid receptor in yeast. Mol Biol Cell 3 1245 1257

60. RicketsonDHostickUFangLYamamotoKRDarimontBD 2007 A conformational switch in the ligand-binding domain regulates the dependence of the glucocorticoid receptor on Hsp90. J Mol Biol 368 729 741

61. BridghamJTBrownJERodrÌguez-MarÌACatchenJMThorntonJW 2008 Evolution of a new function by degenerative mutation in cephalochordate steroid receptors. PLoS Genet 4 e1000191 doi:10.1371/journal.pgen.1000191

62. SimonsSSJ 2006 How much is enough? Modulation of dose-response curve for steroid receptor-regulated gene expression by changing concentrations of transcription factor. Curr Top Med Chem 6 271 285

63. LarkinMABlackshieldsGBrownNPChennaRMcGettiganPA 2007 Clustal W and Clustal X version 2.0. Bioinformatics 23 2947 2948

64. AnisimovaMGascuelO 2006 Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative. Syst Biol 55 539 552

65. JonesDTTaylorWRThorntonJM 1992 The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 8 275 282

66. YangZ 1997 PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13 555 556

67. PondSLFrostSDMuseSV 2005 HyPhy: hypothesis testing using phylogenies. Bioinformatics 21 676 679

68. OtwinowskiZMinorW 1997 Processing of X-ray diffraction data collected in oscillation mode. Methods in enzymology 276 307 326

69. EmsleyPCowtanK 2004 Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60 2126 2132

70. MurshudovGNVaginAADodsonEJ 1997 Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallographica Section D: Biological Crystallography 53 240 255

71. PottertonEBriggsPTurkenburgMDodsonE 2003 A graphical user interface to the CCP4 program suite. Acta Crystallogr D Biol Crystallogr 59 1131 1137

72. ClaudeJBSuhreKNotredameCClaverieJMAbergelC 2004 CaspR: a web server for automated molecular replacement using homology modelling. Nucleic Acids Res 32 W606 9

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Genetika Reprodukčná medicína

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PLOS Genetics


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