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Table 2 Positive selection at amino acid sites of cetacean TLR4

From: Adaptive evolution and functional constraint at TLR4 during the secondary aquatic adaptation and diversification of cetaceans

AA Positionsa PAML Site Model (M8) p> 0.9 PAML Branch-Site Modelc FELd p< 0.2 RELd BF > 50 AA Changes Parallel Changes Property Changese Protein Domain Functional Informationf Cladeg
25      Ser-Arg Yes SM, P, NEU-P.POS LRR3   B, C
28    0.07   Leu-Trp   NP, NEU-P, NEU LRR3   A, D
      Leu-Pro   NP, NEU-SM, NP, NEU    
45    0.16   Thr-Ile Yes SM, P, NEU-NP, NEU LRR4   A, F
104    0.17   Leu-Val   NP, NEU-NP, NEU LRR6   
      Leu-Ser   NP, NEU-SM, P, NEU    
128   0.875    Glu-Pro   P, NEG-SM, NP, NEU LRR7   D
133   0.723    Asn-Lys   SM, P, NEU-P, POS LRR7   G
139   0.708    Gly-Glu   SM, NP, NEU-P, NEG LRR8 Adjacent to site involved in interaction with MD2 G
149   0.565    Ser/Leu -Thr   SM, P, NEU/NP, NEU -SM, P, NEU LRR8   G
150 0.995    228.23 His-Arg Yes P, POS-P, POS LRR8   A, B, C
      His-Asp   P, POS-SM, P, NEG    
177     61.94 Asn-Thr
Asn/Thr
-Ile
Asn-Lys
Ile-Asn
  SM, P, NEU-SM, P, NEU
SM, P, NEU/SM, P, NEU
-NP, NEU
SM, P, NEU-P, POS
NP, NEU-SM, P, NEU
LRR9 Adjacent to site involved in ligand binding and interaction with MD2 A, C, G
179 0.992   0.07 647.96 Lys-Glu
Glu-Gln
Glu/Lys-
Gln
Yes P, POS-P, NEG
P, NEG-P, NEU
P, NEG/P, POS-P, NEU
LRR9   A, C, F
183    0.12 51.06 Arg-Ser
Arg-Thr
  P, POS-SM, P, NEU
P, POS-SM, P, NEU
LRR9   C, D
204      Glu-His Yes P, NEG-P, POS LRR10   A, D
207 1.000   0.08 1563.58 Gly/Lys
-Arg
Arg-Lys
Arg-Thr
Lys-Arg
  SM, NP, NEU/P, POS
-P, POS
P, POS-P, POSP,
POS-SM, P, NEU
P, POS-P, POS
LRR10   A, G, C, E
212      Leu-Val Yes P, POS-NP, NEU LRR10   A, B
221    0.1   Val-Met Yes NP, NEU-NP, NEU LRR11   C, D, F
228 0.994   0.15 544.88 Asp/Ser/Cys
-Asn
Asp-Asn
  SM, P, NEG/SM, P, NEU/SM, NP, NEU
-SM, P, NEU
SM, P, NEG-SM, P, NEU
LRR11   A, G
230 0.978     Gly/Glu/Asp
-Arg
Asp-His
  SM, NP, NEU/P, NEG/SM, P, NEG
-P.POS
SM, P, NEG-P, POS
LRR11   A, E
239     50.32 Cys-Tyr Yes SM, NP, NEU-P, NEU LRR12   B, D, G
247    0.14 86.14 Ile-Thr
Thr-Ile
  NP, NEU-SM, P, NEU
SM, P, NEU-NP, NEU
LRR12 Adjacent to site involved in interaction with ligand binding C, G
250 b 0.936     Asp/Ala
-Lys
Asp/Lys/Ala
-Asn
Asn-Lys
  SM, P, NEG/SM, NP, NEU
-P, POS
SM, P, NEG/P, POS/SM, NP, NEU
-SM, P, NEU
SM, P, NEU-P, POS
LRR12 Ligand binding A, E, G
265      Phe-Leu Yes NP, NEU-NP, NEU LRR13   B, E
272 0.997   0.13 188.28 Gly/Asp-
His
Gly-His
His-Gly
  SM, NP, NEU/SM, P, NEG-P, POS
SM, NP, NEU-P, POS
P, POS-SM, NP, NEU
LRR13 Adjacent to site involved in interaction with ligand binding A, C
280 0.952   0.18 191.07 Glu-Ala
Gln/Glu-
Ala
Yes P, NEG-SM, NP, NEU
P, NEU/P, NEG-SM, NP, NEU
LRR13   A, B, E
302   0.624    His-Arg   P, POS-P.POS LRR14   D
304     55.05 Asp-Asn
Asn-Pro
  SM, P, NEG-SM, P, NEU
SM, P, NEU-SM, NP, NEU
LRR14   G
324 0.996    301.87 Asn-Ser
Asn-Lys
Gly-Asn
  SM, P, NEU-SM, P, NEU
SM, P, NEU-P, POS
SM, NP, NEU-SM, P, NEU
LRR15 Adjacent to site involved in interaction with ligand binding (hydrogen bond) C, E, G
342     53.56 Asn-Ser
Asn/Ser-
Thr
  SM, P, NEU-SM, P, NEU
SM, P, NEU/SM, P, NEU-SM, P, NEU
LRR16 Adjacent to site involved in interaction with ligand binding (hydrogen bond) A
351     0.17 Ile/Ala-Val   NP, NEU/SM, NP, NEU-NP, NEU LRR16 Adjacent to site involved in interaction with ligand binding (hydrophobic interaction) G
368   0.576    Ile-Thr   NP, NEU-SM, P, NEU LRR17 Adjacent to site involved in interaction with ligand binding (hydrophobic interaction) G
404     0.08 Leu-Met   NP, NEU-NP, NEU LRR18   C
408      Ile-Thr Yes NP, NEU-SM, P, NEU LRR19   A, G
409     0.19 Leu/Ile/Phe
-Val
  NP, NEU/NP, NEU/NP, NEU
-NP, NEU
LRR19   A
482     0.16 Ser/Trp-
Phe
Phe/Ser/Trp
-Leu
  SM, P, NEU/P, NEU-NP, NEU
NP, NEU/SM, P, NEU/P, NEU
-NP, NEU
LRR22   A
542 0.903     Met-Thr Yes NP, NEU-SM, P, NEU LRRCT   A, D
551 0.938     Ile-Val
Val-Ile
Yes NP, NEU-NP, NEU
NP, NEU-NP, NEU
Transmembrane   B, F
559     0.16 Val-Ala   NP, NEU-SM, NP, NEU Transmembrane   G
690   0.564    Arg-Gln   P, POS-P, NEU TIR   D
740   0.790    Glu-Asp   P, NEG-SM, P, NEG TIR   G
742   0.697    Asn-Arg   SM, P, NEU-P, POS TIR   G
743     0.18 Gln-Glu   P, NEU-P, NEG TIR   A, F
  1. a Codons identified by more than one ML method were in bold and underlined.
  2. b Site 250 in italic was mapped onto the 3D structure of TLR4, since it directly participates in binding of LPS to TLR4.
  3. c Codons were identified by branch-site model in PAML. Details were in Materials and Methods and Additional file 2: Table S2.
  4. d Codons were estimated in DATAMONKEY.
  5. e SM, small; NP, nonpolar; P, polar; NEU, neutral; POS, positively charged; NEG, negatively charged.
  6. f Codons were in the functional regions predicted by the three-dimensional structure in Shishido et al. 2010. LRR = Leucine-rich repeat, CT = C-terminal, TIR = cytoplasmic Toll/IL-1 receptor
  7. g Amino acid substitutions occurred in the following clades: A = even-toed ungulates, B = river dolphins, C = oceanic dolpins, D = porpoises and white whales, E = sperm whales, F = baleen whales, G = more than one equally parsimonious reconstruction