title: Contrasted evolutionary histories of two Toll-like receptors (Tlr4 and Tlr7) in wild rodents (MURINAE).
abstract: BACKGROUND
  In vertebrates, it has been repeatedly demonstrated that genes encoding proteins involved in pathogen-recognition by adaptive immunity (e.g. MHC) are subject to intensive diversifying selection. On the other hand, the role and the type of selection processes shaping the evolution of innate-immunity genes are currently far less clear. In this study we analysed the natural variation and the evolutionary processes acting on two genes involved in the innate-immunity recognition of Microbe-Associated Molecular Patterns (MAMPs).
  
  
  RESULTS
  We sequenced genes encoding Toll-like receptor 4 (Tlr4) and 7 (Tlr7), two of the key bacterial- and viral-sensing receptors of innate immunity, across 23 species within the subfamily Murinae. Although we have shown that the phylogeny of both Tlr genes is largely congruent with the phylogeny of rodents based on a comparably sized non-immune sequence dataset, we also identified several potentially important discrepancies. The sequence analyses revealed that major parts of both Tlrs are evolving under strong purifying selection, likely due to functional constraints. Yet, also several signatures of positive selection have been found in both genes, with more intense signal in the bacterial-sensing Tlr4 than in the viral-sensing Tlr7. 92% and 100% of sites evolving under positive selection in Tlr4 and Tlr7, respectively, were located in the extracellular domain. Directly in the Ligand-Binding Region (LBR) of TLR4 we identified two rapidly evolving amino acid residues and one site under positive selection, all three likely involved in species-specific recognition of lipopolysaccharide of gram-negative bacteria. In contrast, all putative sites of LBRTLR7 involved in the detection of viral nucleic acids were highly conserved across rodents. Interspecific differences in the predicted 3D-structure of the LBR of both Tlrs were not related to phylogenetic history, while analyses of protein charges clearly discriminated Rattini and Murini clades.
  
  
  CONCLUSIONS
  In consequence of the constraints given by the receptor protein function purifying selection has been a dominant force in evolution of Tlrs. Nevertheless, our results show that episodic diversifying parasite-mediated selection has shaped the present species-specific variability in rodent Tlrs. The intensity of diversifying selection was higher in Tlr4 than in Tlr7, presumably due to structural properties of their ligands.
authors.affiliation: Institute of Vertebrate Biology, Research Facility Studenec, Academy of Sciences, Prague, Czech Republic. Alena.Fornuskova@supagro.inra.fr.
authors.forename: Alena
authors.initials: A
authors.lastname: Fornůsková
authors.forename: Michal
authors.initials: M
authors.lastname: Vinkler
authors.forename: Marie
authors.initials: M
authors.lastname: Pagès
authors.forename: Maxime
authors.initials: M
authors.lastname: Galan
authors.forename: Emmanuelle
authors.initials: E
authors.lastname: Jousselin
authors.forename: Frederique
authors.initials: F
authors.lastname: Cerqueira
authors.forename: Serge
authors.initials: S
authors.lastname: Morand
authors.forename: Nathalie
authors.initials: N
authors.lastname: Charbonnel
authors.forename: Josef
authors.initials: J
authors.lastname: Bryja
authors.forename: Jean-François
authors.initials: JF
authors.lastname: Cosson
mesh_terms: D000818:Animals; D019143:Evolution, Molecular; D007113:Immunity, Innate; D051189:Murinae / Q000145:classification* / Q000235:genetics* / Q000276:immunology; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D013045:Species Specificity; D051197:Toll-Like Receptor 4 / Q000737:chemistry / Q000235:genetics* / Q000276:immunology; D051199:Toll-Like Receptor 7 / Q000737:chemistry / Q000235:genetics* / Q000276:immunology
chemical_list: D051197:Toll-Like Receptor 4; D051199:Toll-Like Receptor 7
references.citation: Nat Rev Genet. 2008 Mar;9(3):165-78
references.pmid: 18227810
references.citation: Bioinformatics. 2010 Oct 1;26(19):2455-7
references.pmid: 20671151
references.citation: PLoS Genet. 2009 Jul;5(7):e1000562
references.pmid: 19609346
references.citation: Lancet Infect Dis. 2005 Mar;5(3):156-64
references.pmid: 15766650
references.citation: Science. 1998 Dec 11;282(5396):2085-8
references.pmid: 9851930
references.citation: Mol Biol Evol. 2011 Nov;28(11):3087-97
references.pmid: 21659570
references.citation: Bioinformatics. 2005 May 15;21(10):2531-3
references.pmid: 15713735
references.citation: BMC Evol Biol. 2012 Jul 24;12:122
references.pmid: 22827462
references.citation: PLoS One. 2012;7(11):e48374
references.pmid: 23144869
references.citation: Front Cell Infect Microbiol. 2013 Feb 12;3:3
references.pmid: 23408095
references.citation: Mol Ecol. 2012 Jul;21(14):3545-61
references.pmid: 22607228
references.citation: Nat Rev Genet. 2010 Jan;11(1):17-30
references.pmid: 19953080
references.citation: Semin Immunol. 2004 Feb;16(1):23-6
references.pmid: 14751760
references.citation: Syst Biol. 2008 Oct;57(5):758-71
references.pmid: 18853362
references.citation: Algorithms Mol Biol. 2010 Feb 03;5:16
references.pmid: 20181081
references.citation: Proc Biol Sci. 2013 Feb 01;280(1756):20122753
references.pmid: 23378666
references.citation: Nature. 2008 Feb 21;451(7181):990-3
references.pmid: 18288193
references.citation: Heredity (Edinb). 2009 May;102(5):506-13
references.pmid: 19174839
references.citation: Nat Protoc. 2009;4(3):363-71
references.pmid: 19247286
references.citation: BMC Evol Biol. 2011 May 28;11:149
references.pmid: 21619680
references.citation: Mol Biol Evol. 2011 May;28(5):1703-15
references.pmid: 21239391
references.citation: Dev Comp Immunol. 2010 Oct;34(10):1035-41
references.pmid: 20470819
references.citation: Proc Biol Sci. 2013 Apr 03;280(1759):20130364
references.pmid: 23554395
references.citation: Methods Mol Biol. 2000;132:365-86
references.pmid: 10547847
references.citation: BMC Bioinformatics. 2007 Aug 20;8:301
references.pmid: 17708757
references.citation: Bioinformatics. 2009 Jun 1;25(11):1451-2
references.pmid: 19346325
references.citation: Genome Biol. 2000;1(1):RESEARCH002
references.pmid: 11104518
references.citation: PLoS One. 2011;6(9):e25118
references.pmid: 21949866
references.citation: Cell. 2007 Sep 7;130(5):906-17
references.pmid: 17803912
references.citation: Clin Microbiol Rev. 2004 Jul;17(3):581-611, table of contents
references.pmid: 15258095
references.citation: Structure. 2011 Apr 13;19(4):447-59
references.pmid: 21481769
references.citation: Science. 2004 Mar 5;303(5663):1526-9
references.pmid: 14976262
references.citation: Mol Immunol. 2009 Feb;46(5):978-90
references.pmid: 18995910
references.citation: Genetics. 2007 Dec;177(4):2277-91
references.pmid: 18073432
references.citation: Proc Natl Acad Sci U S A. 2005 Jun 28;102(26):9247-52
references.pmid: 15956202
references.citation: Mol Biol Evol. 2008 Jul;25(7):1253-6
references.pmid: 18397919
references.citation: Proc Biol Sci. 2010 Apr 7;277(1684):979-88
references.pmid: 20071384
references.citation: Nature. 2009 Apr 30;458(7242):1191-5
references.pmid: 19252480
references.citation: Science. 2003 Feb 14;299(5609):1033-6
references.pmid: 12532024
references.citation: Immunol Cell Biol. 2006 Aug;84(4):333-41
references.pmid: 16834572
references.citation: Lancet Infect Dis. 2007 Aug;7(8):531-42
references.pmid: 17646026
references.citation: J Immunol. 2008 Sep 15;181(6):4354-62
references.pmid: 18768894
references.citation: J Immunol. 2005 May 15;174(10):6518-23
references.pmid: 15879155
references.citation: Bioinformatics. 2001 Aug;17(8):754-5
references.pmid: 11524383
references.citation: Syst Biol. 2012 Dec 1;61(6):1029-47
references.pmid: 22848088
references.citation: Nat Immunol. 2010 May;11(5):373-84
references.pmid: 20404851
references.citation: Bioinformatics. 2008 Dec 1;24(23):2780-1
references.pmid: 18818215
references.citation: Trends Immunol. 2004 Dec;25(12):687-93
references.pmid: 15530840
references.citation: Plant Cell. 2006 Mar;18(3):764-79
references.pmid: 16461584
references.citation: Heredity (Edinb). 2011 May;106(5):727-40
references.pmid: 20823902
references.citation: BMC Evol Biol. 2008 Jul 10;8:199
references.pmid: 18616808
references.citation: J Evol Biol. 2011 Jun;24(6):1232-40
references.pmid: 21418116
references.citation: PLoS One. 2012;7(9):e45011
references.pmid: 23024782
references.citation: Mol Biol Evol. 2006 Oct;23(10):1891-901
references.pmid: 16818476
references.citation: Proc Natl Acad Sci U S A. 2012 May 8;109(19):7421-6
references.pmid: 22532668
references.citation: Heredity (Edinb). 2006 Jan;96(1):7-21
references.pmid: 16094301
references.citation: Tissue Antigens. 2009 Jul;74(1):32-41
references.pmid: 19473320
references.citation: Mol Biol Evol. 2011 Oct;28(10):2731-9
references.pmid: 21546353
references.citation: J Evol Biol. 2003 May;16(3):363-77
references.pmid: 14635837
references.citation: Genome Res. 2011 Mar;21(3):349-56
references.pmid: 21270173
references.citation: Annu Rev Biochem. 2011;80:917-41
references.pmid: 21548780
references.citation: Bioinformatics. 2006 Dec 15;22(24):3096-8
references.pmid: 17110367
references.citation: Proc Natl Acad Sci U S A. 2009 Jun 2;106(22):8799-800
references.pmid: 19470454
references.citation: BMC Genomics. 2008 Feb 01;9:62
references.pmid: 18241342
references.citation: Proc Natl Acad Sci U S A. 2005 Jul 5;102(27):9577-82
references.pmid: 15976025
references.citation: Cell. 2006 Feb 24;124(4):783-801
references.pmid: 16497588
references.citation: J Biol Chem. 2009 May 29;284(22):15052-60
references.pmid: 19321453
references.citation: Nucleic Acids Res. 2010 Jul;38(Web Server issue):W529-33
references.pmid: 20478830
references.citation: BMC Bioinformatics. 2009 Oct 28;10:357
references.pmid: 19863793
references.citation: Gene. 2012 Jul 25;503(2):235-43
references.pmid: 22587897
references.citation: BMC Evol Biol. 2010 Jun 18;10:184
references.pmid: 20565819
references.citation: Annu Rev Biochem. 2002;71:635-700
references.pmid: 12045108
references.citation: Crit Rev Immunol. 1997;17(2):179-224
references.pmid: 9094452
references.citation: Nat Immunol. 2012 May 18;13(6):535-42
references.pmid: 22610250
references.citation: Clin Exp Immunol. 2007 Feb;147(2):199-207
references.pmid: 17223959
references.citation: PLoS One. 2011;6(11):e26357
references.pmid: 22073158
references.citation: Clin Microbiol Rev. 2003 Oct;16(4):637-46
references.pmid: 14557290
references.citation: Trends Immunol. 2009 Mar;30(3):124-30
references.pmid: 19211304
references.citation: Proc Natl Acad Sci U S A. 2004 Mar 9;101(10):3490-4
references.pmid: 14990802
references.citation: PLoS Genet. 2012;8(7):e1002764
references.pmid: 22807683
references.citation: Immunogenetics. 2006 Apr;58(2-3):191-202
references.pmid: 16467985
references.citation: Immunogenetics. 2008 May;60(5):249-56
references.pmid: 18415094
references.citation: Mol Biol Evol. 2010 Sep;27(9):2172-86
references.pmid: 20410160
references.citation: Mol Ecol. 2013 Feb;22(4):1019-34
references.pmid: 23278980
references.citation: Science. 2004 Mar 5;303(5663):1529-31
references.pmid: 14976261
references.citation: Autoimmun Rev. 2009 Mar;8(5):400-4
references.pmid: 19162250
references.citation: Proc Natl Acad Sci U S A. 2007 Oct 16;104(42):16645-50
references.pmid: 17925445
references.citation: J Immunol. 2008 Jul 15;181(2):1245-54
references.pmid: 18606678
references.citation: Evolution. 2012 Mar;66(3):720-731
references.pmid: 22380435
references.citation: Immunol Rev. 2009 Jan;227(1):264-82
references.pmid: 19120490
references.citation: Evolution. 1995 Aug;49(4):718-726
references.pmid: 28565131
references.citation: Trends Ecol Evol. 2001 Jul 1;16(7):358-364
references.pmid: 11403868
references.citation: Protein Sci. 2009 Aug;18(8):1684-91
references.pmid: 19521997
references.citation: Genetics. 1993 Aug;134(4):1289-303
references.pmid: 8375663
references.citation: Nature. 1997 Jul 24;388(6640):394-7
references.pmid: 9237759
references.citation: Immunol Rev. 2007 Dec;220:251-69
references.pmid: 17979852
references.citation: BMC Evol Biol. 2011 Dec 20;11:368
references.pmid: 22185391
references.citation: Immunity. 2011 May 27;34(5):680-92
references.pmid: 21616437
references.citation: Immunol Rev. 2008 Jun;223:271-83
references.pmid: 18613842
references.citation: Proc Natl Acad Sci U S A. 1998 May 26;95(11):5857-64
references.pmid: 9600884
references.citation: Immunity. 2004 Nov;21(5):607-15
references.pmid: 15539148
references.citation: Trends Ecol Evol. 2006 Aug;21(8):433-8
references.pmid: 16764966
references.citation: J Immunol. 2010 Jun 15;184(12):6993-7000
references.pmid: 20483729
references.citation: Am J Hum Genet. 2003 Nov;73(5):1162-9
references.pmid: 14574645