Figure 1.
Taxonomic lineage of homologs to the HET-s PFD.
The expanded taxonomic lineage of all species is presented. Actual species of HET-s PFD homologs are highlighted in bold and underlined. The non-significant PFD homologs from Arthroderma otae and Grosmannia clavigera (red boxes) are also included for comparison.
Figure 2.
Graphical representation of the similarity matrix between N- and C-terminal homologs of the PFD.
Each point on the graph represents the percent similarity of the C-terminal domains and the N-terminal domains for a pair of PFD homologs. In addition to HET-s, ten PFD homologs are represented. Pairs of homologs that include the HET-s or HET-S proteins have been colored differently for comparison. Comparison of Podospora anserina sequences to each other are circled (purple).
Figure 3.
Phylogenetic trees of homologs to the HET-s prion-forming and N-terminal domains.
A) Phylogenetic tree of homologs to the HET-s prion-forming domain. B) Phylogenetic tree of homologs to the HET-s N-terminal domain. The generated trees are neighbor-joining majority-rule consensus trees composed of 11 sequences. Sequences starting with EEU represent Nectria haematococca mpVI 77-13-4, FOXG represent Fusarium oxysporum f. sp. lycopersici, FVEG represent Fusarium verticillioides (Gibberella moniliformis), and FG represent Fusarium graminearum (Gibberella zeae). Branch numbers indicate the number of times the partition of the species into two sets which are separated by that branch occurs among the trees, out of 100 trees, as described by Phylip consense program [33].
Table 1.
HET-s homologs showing significant structural homology to the 2RNM solenoid.
Figure 4.
Models of HET-s homologs with structural homology to the HET-s PFD.
The original solenoid [PDB: 2RNM] [6], [7] is shown in the top left corner. Ten structural homologs are represented, including the small s protein homolog from G. calivigera. The structure of FG10600.1 has been shown by Wasmer et al [10] and is not included here. For each structure, two rungs for each solenoid are represented, with the first rung at the top. Amino acids are color-coded as follows: acidic (Asp, Glu) in red, basic (Arg, Lys, His) in blue, nonpolor (Met, Phe, Pro, Trp, Val, Leu, Ile, Ala) in white, polar (Ser, Thr, Asn, Gln, Tyr) in green, and the protein backbone in yellow.
Figure 5.
Conserved physicochemical properties of the HET-s structure in homologous solenoid models.
The three chains of 2RNM (A, C, D), used as templates in MODELLER, are represented (top). Beta sheet positions (as rendered in PyMOL) are highlighted in yellow (unless colored to represent other physicochemical properties), and helices are highlighted in red. The three salt bridge pairs (K229-E265, E234-K270, R236-E272) of HET-s are highlighted in dark blue, light blue, and light green, respectively. Asparagine ladders are represented in red boxes. The same coloring scheme has been adapted to the 11 generated models against the HET-s solenoid structure. The small s protein from G. clavigera (here, represented as Grosmannia), is also included for comparison against its 2rnm:A template. For all models, gapped positions have been removed for clarity, and the number of amino acids spanning the HET-s PFD are indicated (out of 72 residues). The secondary structure of each model has been placed above each sequence. Beta-strands are represented by yellow arrows and alpha-helices by red boxes. Blank spaces between the yellow arrows represent β arcs within each solenoid rung, and the long connecting loop between the two solenoid rungs in each model has been represented by a grey flat line.
Figure 6.
Taxonomic lineage of homologs to the N-Term domain.
Species with proteins homologous to the prion domain are highlighted in the red box. The marginal additional homologs observed in Grosmannia clavigera and Arthroderma otae are highlighted in the navy boxes.
Figure 7.
Classification of 65 SCOP domains into superfamilies.
These are the SCOP domain superfamilies that co-occur with the HET-s protein domains. Ten superfamilies are represented.
Figure 8.
SUPERFAMILY associations with the N-terminal homologs (n = 36).
A majority-rule consensus tree is generated for N-terminal homologs which are significantly associated with families identified using SUPERFAMILY. The clades of the different proteins are also annotated, especially for proteins which belong to ‘Sordariomycetes’ or ‘Eurotiomycetes’. Superfamilies associated with each protein are indicated, and are abbreviated as follows: CTCR: C-term (heme d1) of cytochrome reductase. P-loop NTH: P-loop containing nucleoside triphosphate hydrolase. NDST: Nucleoside-diphospho-sugar transferase.