Figure 1
TOC1 and PRR phylogeny. UPGMA phylogenetic tree of TOC1/PRR proteins. The groupings are strongly supported, as indicated by high bootstrap values (>70%). The scale bar represents 0.05 estimated amino-acid change per sequence position. Sequences in red were selected for further analysis in this study. Pt, Populus trichocarpa; Cs, Castanea sativa; At, Arabidopsis thaliana; Vv, Vitis vinifera Lj, Lotus japonicus; Mc, Mesembryanthemum crystallinum; Os, Oryza sativa. Sequence origin can be found in the Methods section.
Figure 2
Global alignment of selected TOC1 sequences. ClustalW multiple alignment of TOC1 amino-acid sequences chosen based on the phylogenetic analysis in Figure 1. The three colors (green, red and blue) represent the modular domains for the four TOC1 sequences that were selected for further analysis by defining regions in sequence that move from conservation to non-conservation. The conservation block highlights the percentage identity of amino-acids in the lineup. Note that for module I and module III, there is far more identity than in module II. Abbreviations refer to: At, Arabidopsis thaliana; Cs, Castanea sativa; Lj, Lotus japonicus; Mc, Mesembryanthemum crystallinum; Os, Oryza sativa; Pt, Populus trichocarpa; Vv, Vitis vinifera
Figure 3
Models of module I. Structural models of module I (left) and aligned with the Arabidopsis domain I (right). For the images at the left, the colors from blue to red represent sequence length from an amino- to carboxy-terminal direction. For the aligned figures at the right, the Arabidopsis module I is colored green in contrast to a red color for the compared alignment.
Figure 4
Comparison of module I to response regulators from bacteria. (A) Multiple alignment of module I from plants and response regulators from bacteria. Ec, Escherichia coli CheY; Bs, Bacillus subtilis SPO0F. The lineup is as described in Figure 2. (B) Structures of the Arabidopsis model for module I and published structures for two response regulators (left) and aligned with to Arabidopsis module I (right). Coloration is as shown.
Table 1
The table summarizes the number of selected cluster-center modules chosen from the starting point of 500 generated ROSETTA structures (see Methods).
| Module I | Module II | Module III | |
| AtTOC1 | 3 | 10 | 10 |
| CsTOC1 | 4 | 8 | 3 |
| LjTOC1 | 5 | 9 | 9 |
| McTOC1 | 3 | 10 | 8 |
Figure 5
Models of module II. Structural models of module II. The colors from blue to red represent sequence length from the amino- to carboxy-terminal direction.
Figure 6
Models of module III in predictive complex with calcium. Structural models of module III. The colors from blue to red represent sequence length from the amino- to carboxy-terminal direction. Note that alpha-helical clusters in the carboxy terminus center these structures, and that a calcium ion can be fit into all four structures in an amino-terminal position within all structures. The red arrow points to the fit calcium, which is colored as a gray sphere.
Figure 7
Comparison of CCT sub-module structures. From left to right, the predicted structures of the CCT sub-module of CO and AtTOC1, and their alignment match when aligned. The colors from blue to red represent sequence length from the amino- to carboxy-terminal direction.
Figure 8
Schematic representation of a TOC1 structural model. I PRR domain – this resembles bona fide response regulators. II Linker domain – a putative bridge between modules I and III. III Calcium-binding domain – a potential sensor for a metal. IIIb Protein-binding domain – a potential interaction motif for HAP DNA-binding factors.