Table 2.
Characteristics of amino acid replacements under positive selection in the C4 lineages of Suaedoideae
| AA no.a | AA change C3→C4 | Type of changeb | ΔHc | ΔPd | ΔVe | SAf (%) | ΔGg (kJ mol–1) | No. of C3/ no. of C4 h | No. of transitions for C4 AA | No. of transversions for C4 AA | Location of residue |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 480 | D→E | D→D | 0.0 | –0.7 | 27.3 | 92.7 | S (0.15) | 0/11 | – | 1 | α-Helix 18 |
| 485i | K→A | R→A | 5.7 | –3.2 | –80.0 | 40.3 | DS (–1.12) | 0/7 | 1 | 1 | α-Helix 19 |
| 513 | D→A | D→A | 5.3 | –4.9 | –22.5 | 18.7 | DS (–1.17) | 0/9 | – | 1 | α-Helix 20 |
| 519j | H→K | R→R | –0.7 | 0.9 | 15.4 | 46.7 | S (2.04) | 0/2 | – | 2 | α-Helix 20 |
| 627 | V→I | A→A | 0.3 | –0.7 | 26.7 | 10.3 | S (1.4) | 0/9 | 1 | – | α-Helix 25 |
| 662 | D→E | D→D | 0.0 | –0.7 | 27.3 | 45.1 | DS (–1.11) | 0/3 | – | 1 | Loop |
| 695 | T→V | P→A | 4.9 | –2.7 | 23.9 | 0.7 | DS (–4.39) | 0/1 | 2 | – | α-Helix 28 |
| T→I | P→A | 5.2 | –3.4 | 50.6 | 0.7 | DS (–0.97) | 0/1 | 1 | α-Helix 28 | ||
| 707 | I→M | A→A | –2.6 | 0.5 | –3.8 | 47.6 | DS (–0.64) | 0/1 | 1 | – | Loop |
| I→L | A→A | –0.7 | –0.3 | 0.0 | 47.6 | DS (–1.55) | 0/2 | – | 1 | Loop | |
| I→S | A→P | –5.3 | 4.0 | –77.7 | 47.6 | S (0.38) | 0/1 | 1 | – | Loop | |
| I→T | A→P | –5.2 | 3.4 | –50.6 | 47.6 | DS (–0.3) | 0/1 | 1 | – | Loop | |
| 733 | F→M | F→A | –0.9 | 0.5 | –27.0 | 39.9 | DS (–3.73) | 0/2 | 1 | 1 | Loop |
| F→L | F→A | 1.0 | –0.3 | –23.2 | 39.9 | DS (–3.14) | 0/8 | – | 1 | Loop | |
| F→R | F→R | –7.3 | 5.3 | –16.5 | 39.9 | DS (–2.42) | 0/2 | 1 | 1 | Loop | |
| 735i | E→N | D→P | 0.0 | –0.7 | –24.3 | 48.7 | DS (–0.76) | 0/7 | 1 | 1 | Loop |
| 744 | L→C | A→P | –1.3 | 0.6 | –58.2 | 29.5 | DS (–2.63) | 0/2 | – | 2 | α-Helix 30 |
| L→R | A→R | –8.3 | 5.6 | 6.7 | 29.5 | DS (–4.14) | 0/2 | – | 1 | α-Helix 30 | |
| 780 | A→S | A→P | –2.6 | 1.1 | 0.4 | 0.0 | DS (–3.1) | 0/4 | – | 1 | α-Helix 32 |
| 794 | F→I | F→A | 1.7 | 0.0 | –23.2 | 0.0 | DS (–2.03) | 0/6 | – | 1 | α-Helix 34 |
| F→M | F→A | –0.9 | 0.5 | –27.0 | 0.0 | DS (–2.51) | 0/2 | 1 | 1 | α-Helix 34 | |
| F→L | F→A | 1.0 | –0.3 | –23.2 | 0.0 | DS (–0.87) | 0/1 | – | 1 | α-Helix 34 | |
| 863 | S→K | A→R | 0.6 | 2.1 | 79.6 | 15.7 | DS (–0.22) | 0/1 | 1 | 1 | α-Helix 38 |
| S→D | A→D | –2.7 | 3.8 | 22.1 | 15.7 | S (0.07) | 0/1 | 2 | – | α-Helix 38 | |
| S→N | A→P | –2.7 | 2.4 | 5.1 | 15.7 | S (2.2) | 0/9 | 1 | – | α-Helix 38 | |
| S→T | P→P | 0.1 | –0.6 | 27.1 | DS (–0.43) | 0/1 | – | 1 | α-Helix 38 | ||
| 868 | K→R | R→R | –0.6 | –0.8 | 4.8 | 16.5 | DS (–0.58) | 0/2 | 1 | – | α-Helix 38 |
| K→Q | R→P | 0.4 | –0.8 | –24.8 | 16.5 | DS (–0.07) | 0/1 | – | 1 | α-Helix 38 | |
| K→L | R→A | 7.7 | –3.4 | –1.9 | 16.5 | DS (–0.88) | 0/7 | – | 2 | α-Helix 38 | |
| 880 | D→N | D→P | 0.0 | –1.4 | 3.0 | 46.5 | DS (–1.49) | 0/5 | 1 | – | Loop |
| D→E | D→D | 0.0 | –0.7 | 27.3 | 46.5 | DS (–0.22) | 0/1 | – | 1 | Loop | |
| D→Y | D→A | 2.2 | –6.8 | 82.5 | 46.5 | DS (–3.79) | 0/1 | – | 1 | Loop | |
| 931 | M→I | A→A | 2.6 | –0.5 | 3.8 | – | – | 0/2 | 1 | – | α-Helix 39 |
a Amino acid (AA) numbering is based on the maize sequence after Hudspeth and Grula (1989).
b Side chain type changes: A, non-polar aliphatic; P, polar uncharged; D, polar negatively charged; R, polar positively charged.
c Hydropathicity difference (Kyte and Doolittle, 1982).
d Polarity difference (Grantham, 1974).
e van der Waals volume difference (Zamyatin, 1972).
f Solvent accessibility calculated using the Flaveria trinervia ppc-2 structure (pdb file 3ZGE) by CUPSAT (Parthiban et al. 2006).
g Overall stability of the protein predicted using the F. trinervia ppc-2 structure (pdb file 3ZGE) by CUPSAT (Parthiban et al., 2006): DS, destabilizing; S, stabilizing.
h Number of C3 or C4 Suaedoideae species that have the indicated amino acid substitution (amino acid on right side of arrow).
i Specific for Salsina Kranz anatomy.
j Specific for Schoberia Kranz anatomy.