Table 1.
Structural changes implicated in phenotypic variation and evolution in plants.
| Organism | Protein | Trait | Amino acid change | Scale* | Reference |
|---|---|---|---|---|---|
| Altered active or binding site | |||||
| Arabidopsis thaliana | Cytochrome P450’s | Arabidopyrone synthesis | Gradual replacement | M | Weng et al. (2012) |
| Boechera stricta | CYP79F1 duplicates | Glucosinolate biosynthesis | G134L, P536K | M | Prasad et al. (2012) |
| Eleusine indica | α-tubulin | Herbicide resistance | T239I | m | Yamamoto et al. (1998) |
| Ipomoea spp. | Dfr | Flower color | Five amino acid sites | M | Smith et al. (2013) |
| Oryza sativa | SH4 | Seed abscission | K80N, DNA-binding domain | m | Li et al. (2006) |
| Setaria viridis | α-tubulin | Herbicide resistance | T239I | m | Anthony et al. (1998) |
| Solanum lycopersicum | LIN5 | Sucrose metabolism | E348D, close proximity to catalytic site | m | Fridman et al. (2004) |
| Asteraceae | HHS | Pyrrolizidine alkaloid synthesis | Gradual replacement | M | Anke et al. (2004) |
| Convolvulaceae | HHS | Pyrrolizidine alkaloid synthesis | Gradual replacement | M | Kaltenegger et al. (2013) |
| Flowering plants | psbA | Herbicide resistance | S264G | m | Powles and Yu (2010) |
| Flowering plants | AHAS | Herbicide resistance | Seven amino acid sites | m | Powles and Yu (2010) |
| Land plants | LEAFY | Vegetative to reproductive transition | Gradual replacement | M | Maizel et al. (2005) |
| Eukaryotes | MADS TF’s | Morphogenesis | Gradual replacement | M | Gramzow et al. (2010) |
| Altered protein–protein interactions | |||||
| Antirrhinum majus | FAR, PLE | Floral organ identity | Q insertion (K-C domain junction) | M | Airoldi et al. (2010) |
| Arabidopsis thaliana | ATMYC1 | Trichome density | P189A | m | Symonds et al. (2011) |
| Arabidopsis thaliana (Cvi) | PHYB | Light response | I143L (PPI domain) | m | Filiault et al. (2008) |
| Arabidopsis thaliana | AGL6 | Branching | P201L (C-terminal) | m | Huang et al. (2012) |
| Helianthus annuus | FT | Flowering time | Frameshift mutation, 17aa insertion | m | Blackman et al. (2010) |
| Hordeum vulgare | PPD-H1 | Flowering time | G588W in the CCT domain | m | Turner et al. (2005) |
| Medicago | SHP homologs | Fruit morphology | S insertion (C-terminal) | M | Fourquin et al. (2013) |
| Thalictrum thalictroides | C class MADS TF | Floral organ identity | 8 or 13 amino acid deletion, Keratin-like domain | m | Galimba et al. (2012) |
| Triticum aestivum | Q | Seed free-threshing | I329V | m | Simons et al. (2006) |
| Land plants | DELLA | GA-mediated growth responses | Gradual changes to DELLA, affecting DELLA-GID1 PPI | M | Yasumura et al. (2007) |
| Flowering plants | B class MADS TF | Floral development | Uncharacterized | M | Winter et al. (2002) |
| Altered domain content | |||||
| Arabidopsis thaliana (Cvi) | ANAC089 | Fructose sensitivity | Truncated protein, membrane-anchoring domain lost. | m | Li et al. (2011) |
| Core eudicots | EuAP3 and TM6 | Floral development | Frameshift mutation, novel C-terminal | M | Kramer et al. (2006) |
| Core eudicots | EuAP1 and EuFUL | Floral development | Frameshift mutation, novel C-terminal | M | Litt and Irish (2003); Pabón-Mora et al. (2012) |
| Grasses (Oryza sativa) | OsMADS5 | Floral morphology | Truncated protein, C-terminal lost | M | Christensen and Malcomber (2012) |
| Land plants | Terpene synthases | Secondary metabolism | γ-domain lost | M | Hillwig et al. (2011) |
| Green plants | AP2 domain | Development, stress response | HGT of novel domain | M | Magnani et al. (2004) |
| Green plants | MEKHLA domain | Development | HGT of novel domain | M | Mukherjee and Buerglin (2006) |
| Altered activity as an activator or repressor | |||||
| Beta vulgaris | BvFT1, BvFT2 | Flowering, vernalization | Three amino acids in segment B | M | Pin et al. (2010) |
| Glycine max | Ln | Leaf morphology | D9H, EAR transcriptional repression motif | m | Jeong et al. (2012) |
| Zea mays | TGA1 | Inflorescence morphology | K8N | m | Wang et al. (2005) |
| Angiosperms (Arabidopsis thaliana) | TFL, FT | Flowering | Y85H (FT to TFL), H88Y (TFL to FT) | M | Hanzawa et al. (2005) |
| Altered protein stability | |||||
| Arabidopsis thaliana (Lm-2) | PHYA | Light response | M548T | m | Maloof et al. (2001) |
| Arabidopsis thaliana (Cvi) | CRY2 | Light response | V367M | m | El-Assal et al. (2001) |
| Arabidopsis thaliana | ETC2 | Trichome density | K19E | m | Hilscher et al. (2009) |
| Hypomorphic and hypermorphic alleles | |||||
| Arabidopsis thaliana (Cvi) | HMA5 | Cu tolerance | Missense mutations in conserved transmembrane domain | m | Kobayashi et al. (2008) |
| Arabidopsis thaliana | HMA3 | Cd accumulation | Missense mutations at ATP-binding site (or nearby) | m | Chao et al. (2012) |
| Arabidopsis thaliana (Shahdara) | APR2 | Sulfate accumulation | A399E | m | Loudet et al. (2007) |
| Arabidopsis thaliana | ACD6 | Late onset necrosis, leaf initiation | Two or three aa replacements in transmembrane domain | m | Todesco et al. (2010) |
| Arabidopsis thaliana (Sy-0) | HUA2 | Plant architecture | K525E | m | Wang et al. (2007) |
| Oryza sativa | SKC1 | Salt tolerance | Four amino acids, transmembrane domain | m | Ren et al. (2005) |
| Uncertain function | |||||
| Arabidopsis lyrata | FRI-like | Flowering | 14 aa insertion | m | Kuittinen et al. (2008) |
| Oryza sativa | PROG1 | Plant architecture (tillering) | T152S | m | Jin et al. (2008) |
*
M = macroevolutionary scale, m = microevolutionary scale.