Figure 3. Orientation-switch III mutations in oncogenic Ras isoforms that are reported in cancer genome databases.
Cancer-associated point mutations (missense, nonsense, and silent) in the orientation-switch III regions as reported in COSMIC, cBioPortal, and ICGC databases. Schematic representations of the linear protein structures of (A) H-ras, (B) N-ras, and (C) K-ras. Critical functional regions in the structures are annotated; those of the orientation-switch III by ovals. Approximate position of hot-spot mutation residues (G12, G13, and Q61) is marked with red triangles. Mutations from cancer patient samples are boxed, RASopathy mutations are boxed and in italics, other annotated mutations are from cancer cell lines (Prior et al., 2012). Mutations that are studied here are highlighted in yellow. See also Figure 3—figure supplement 1.
Figure 3—figure supplement 1. Phylogenetic analysis of the Ras switch III region.
(A) ClustalW sequence alignment of 18 Ras proteins from different species as annotated on the left. Consensus sequence is shaded in dark and switch III region elements β2-β3-loop (residues 40–56) and helix α5 (residues 152–166) are highlighted with a black frame. (B) Unrooted phylogenetic trees were built from these proteins for the β2-β3-loop and (C) helix α5. (B, C) Numbers on internal branches indicate the percentage of 1000 bootstrap trials that support the branch (numbers <70% are omitted). Residues outside the region of interest were excluded using the position-masking tool for both phylogenetic analyses. The analysis revealed that switch III residues are highly conserved among all analyzed Ras proteins. The human Ras isoforms cluster together with other Ras proteins from the Bilateria species (D. rerio, X. laevis, S. mansoni, M. edulis, D. melanogaster, and C. elegans). Ras proteins from the Fungi kingdom (S. pombe and T. hirsuta) and Cnidaria phylum (H. vulgaris) species show a divergent pattern that corresponds to the speciation events that occurred in the course of evolution (∼1298 Ma for Bilateria—Cnidaria and ∼1513 Ma for Animalia—Fungi speciation event) (Hedges et al., 2004).