title: Regulatory evolution through divergence of a phosphoswitch in the transcription factor CEBPB.
abstract: There is an emerging consensus that gene regulation evolves through changes in cis-regulatory elements and transcription factors. Although it is clear how nucleotide substitutions in cis-regulatory elements affect gene expression, it is not clear how amino-acid substitutions in transcription factors influence gene regulation. Here we show that amino-acid changes in the transcription factor CCAAT/enhancer binding protein-β (CEBPB, also known as C/EBP-β) in the stem-lineage of placental mammals changed the way it responds to cyclic AMP/protein kinase A (cAMP/PKA) signalling. By functionally analysing resurrected ancestral proteins, we identify three amino-acid substitutions in an internal regulatory domain of CEBPB that are responsible for the novel function. These amino-acid substitutions reorganize the location of key phosphorylation sites, introducing a new site and removing two ancestral sites, reversing the response of CEBPB to GSK-3β-mediated phosphorylation from repression to activation. We conclude that changing the response of transcription factors to signalling pathways can be an important mechanism of gene regulatory evolution.
authors.affiliation: Yale Systems Biology Institute and Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06511, USA. vincent.j.lynch@yale.edu
authors.forename: Vincent J
authors.initials: VJ
authors.lastname: Lynch
authors.forename: Gemma
authors.initials: G
authors.lastname: May
authors.forename: Günter P
authors.initials: GP
authors.lastname: Wagner
mesh_terms: D019943:Amino Acid Substitution; D000818:Animals; D022782:CCAAT-Enhancer-Binding Protein-beta / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D000242:Cyclic AMP / Q000378:metabolism; D017868:Cyclic AMP-Dependent Protein Kinases / Q000378:metabolism; D019143:Evolution, Molecular; D005260:Female; D000071161:Forkhead Box Protein O1; D051858:Forkhead Transcription Factors / Q000378:metabolism; D005786:Gene Expression Regulation; D038362:Glycogen Synthase Kinase 3 / Q000378:metabolism; D000071679:Glycogen Synthase Kinase 3 beta; D006367:HeLa Cells; D006801:Humans; D008322:Mammals; D008958:Models, Molecular; D010766:Phosphorylation / Q000235:genetics; D010920:Placenta; D011247:Pregnancy; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D013329:Structure-Activity Relationship
chemical_list: D022782:CCAAT-Enhancer-Binding Protein-beta; C545012:CEBPB protein, human; C085126:FOXO1 protein, human; D000071161:Forkhead Box Protein O1; D051858:Forkhead Transcription Factors; D000242:Cyclic AMP; C000605506:GSK3B protein, human; D000071679:Glycogen Synthase Kinase 3 beta; D017868:Cyclic AMP-Dependent Protein Kinases; D038362:Glycogen Synthase Kinase 3
references.citation: EMBO J. 2010 Mar 17;29(6):1105-15
references.pmid: 20111005
references.citation: Proc Natl Acad Sci U S A. 2004 Aug 31;101(35):12986-91
references.pmid: 15317935
references.citation: Nat Rev Genet. 2007 Mar;8(3):206-16
references.pmid: 17304246
references.citation: Mol Endocrinol. 2002 Jan;16(1):141-54
references.pmid: 11773445
references.citation: Proc Natl Acad Sci U S A. 2010 Jun 8;107(23):10555-60
references.pmid: 20498049
references.citation: J Biol Chem. 2010 Jul 9;285(28):21399-410
references.pmid: 20452968
references.citation: J Biol Chem. 2002 Jun 7;277(23):20825-32
references.pmid: 11893744
references.citation: Nature. 2002 Feb 21;415(6874):910-3
references.pmid: 11859369
references.citation: Genes Dev. 1991 Oct;5(10):1754-66
references.pmid: 1655570
references.citation: J Biol Chem. 2005 Sep 23;280(38):32683-92
references.pmid: 16055922
references.citation: Evolution. 2000 Aug;54(4):1079-91
references.pmid: 11005278
references.citation: Genes Dev. 1994 Nov 15;8(22):2781-91
references.pmid: 7958933
references.citation: Mol Immunol. 2007 Feb;44(6):1384-92
references.pmid: 16784777
references.citation: Proteins. 2008 Mar;70(4):1357-66
references.pmid: 17879262
references.citation: PLoS Biol. 2005 Jul;3(7):e245
references.pmid: 16000021
references.citation: J Exp Zool B Mol Dev Evol. 2005 Nov 15;304(6):580-92
references.pmid: 16252266
references.citation: J Biol Chem. 1995 Jun 23;270(25):15130-6
references.pmid: 7797496
references.citation: Proc Natl Acad Sci U S A. 2008 Sep 30;105(39):14928-33
references.pmid: 18809929
references.citation: Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W526-31
references.pmid: 15215442
references.citation: Sci Signal. 2009 Feb 24;2(59):ra8
references.pmid: 19244213
references.citation: EMBO J. 1995 Jul 3;14(13):3170-83
references.pmid: 7621830
references.citation: Evolution. 2008 Sep;62(9):2155-77
references.pmid: 18616572
references.citation: Evolution. 2008 Sep;62(9):2131-54
references.pmid: 18564379
references.citation: Proc Natl Acad Sci U S A. 2007 May 15;104 Suppl 1:8605-12
references.pmid: 17494759
references.citation: Curr Biol. 2001 Sep 18;11(18):1403-12
references.pmid: 11566098
references.citation: Curr Biol. 2010 Jan 26;20(2):R48-52
references.pmid: 20129035
references.citation: Nature. 2002 Feb 21;415(6874):914-7
references.pmid: 11859370
references.citation: Curr Opin Genet Dev. 2003 Apr;13(2):199-206
references.pmid: 12672498
references.citation: Cell. 2008 Jul 11;134(1):25-36
references.pmid: 18614008
references.citation: J Biol Chem. 1999 Aug 27;274(35):24808-18
references.pmid: 10455153