Human RAS superfamily proteins and related GTPases

Abstract

The tumor oncoproteins HRAS, KRAS, and NRAS are the founding members of a larger family of at least 35 related human proteins. Using a somewhat broader definition of sequence similarity reveals a more extended superfamily of more than 170 RAS-related proteins. The RAS superfamily of GTP (guanosine triphosphate) hydrolysis-coupled signal transduction relay proteins can be subclassified into RAS, RHO, RAB, and ARF families, as well as the closely related Galpha family. The members of each family can, in turn, be arranged into evolutionarily conserved branches. These groupings reflect structural, biochemical, and functional conservation. Recent findings have provided insights into the signaling characteristics of representative members of most RAS superfamily branches. The analysis presented here may serve as a guide for predicting the function of numerous uncharacterized superfamily members. Also described are guanosine triphosphatases (GTPases) distinct from members of the RAS superfamily. These related proteins employ GTP binding and GTPase domains in diverse structural contexts, expanding the scope of their function in humans.

Fig. 1

RAS proteins exist in equilibrium between GTP- and GDP-bound forms. GEFs and GAPs regulate the relative amounts of each form. The GTP-bound conformation of RAS shows high-affinity interactions with effector proteins that propagate downstream signaling.

Fig 2

Alignment of human RAS subfamily members. G box consensus residues are highlighted in blue. N- and C-terminal region cysteines, some of which are substrates for prenylation or fatty acid modification, are highlighted in green. N-terminal glycines in positions favoring myristoylation are highlighted in yellow. C-terminal basic residues are highlighted in pink. Gray highlighting indicates residues that are highly conserved in 90% of members. Amino acids omitted for optimum alignment are indicated with the “^” symbol. For KRAS, the KRAS2B isoform sequence is presented. See Table 1 for alternate gene symbols.

Fig 2

Alignment of human RAS subfamily members. G box consensus residues are highlighted in blue. N- and C-terminal region cysteines, some of which are substrates for prenylation or fatty acid modification, are highlighted in green. N-terminal glycines in positions favoring myristoylation are highlighted in yellow. C-terminal basic residues are highlighted in pink. Gray highlighting indicates residues that are highly conserved in 90% of members. Amino acids omitted for optimum alignment are indicated with the “^” symbol. For KRAS, the KRAS2B isoform sequence is presented. See Table 1 for alternate gene symbols.

Fig. 3

Dendrogram of RAS subfamily members from H. sapiens, D. melanogaster (Dm), and C. elegans (Ce). Human protein names are in uppercase letters. Branch lengths are directly proportional to the number of differences between sequences compared. See Table 1 for alternate names for human protein.

Fig 4

Alignment of human RHO subfamily members. Highlighting and symbols are as in Fig. 2. Large C-terminal sequence extensions for RHOBTB and RHOT proteins have been removed (indicated by the “#” symbol). See Table 1 for alternate gene symbols.

Fig. 5

Dendrogram of RHO subfamily members from H. sapiens, D. melanogaster, and C. elegans. RHOT1-N and RHOT2-N represent the N-terminal GTPase domains of RHOT1 and RHOT2. Human protein names are in uppercase letters.

Fig. 6

Alignment of human RAB subfamily members. Highlighting and symbols are as in Fig. 2. See Table 1 for alternate gene symbols. 201475 (LOC201475, gi41150884) represents an unannotated gene and matching cDNA. The RAB42 sequence is derived from an N-terminal truncated message.

Fig. 6

Alignment of human RAB subfamily members. Highlighting and symbols are as in Fig. 2. See Table 1 for alternate gene symbols. 201475 (LOC201475, gi41150884) represents an unannotated gene and matching cDNA. The RAB42 sequence is derived from an N-terminal truncated message.

Fig. 6

Alignment of human RAB subfamily members. Highlighting and symbols are as in Fig. 2. See Table 1 for alternate gene symbols. 201475 (LOC201475, gi41150884) represents an unannotated gene and matching cDNA. The RAB42 sequence is derived from an N-terminal truncated message.

Fig. 7

Dendrogram of RAB subfamily members from H. sapiens and D. melanogaster. Human protein names are in uppercase letters.

Fig. 8

Alignment of human ARF subfamily members. Highlighting and symbols are as in Fig. 2. See Table 1 for alternate gene symbols. The following are unannotated genes with matching cDNAs: 339231 (LOC339231, gi 42661282), 344988 (LOC344988, gi 37539816), and DKFZp761 (DKFZp761H079, gi 33598955).

Fig. 9

Dendrogram of ARF subfamily members from H. sapiens, D. melanogaster, and C. elegans. Human protein names are in uppercase letters.

Fig. 10

Alignment of human Gα subfamily members. Highlighting and symbols are as in Fig. 2. Insert sequences (relative to RAS subfamily proteins) have been removed and are indicated with “^”. See Table 1 for alternate gene symbols.

Fig. 11

Dendrogram of Gα subfamily members from H. sapiens, D. melanogaster, and C. elegans. Human protein names are in uppercase letters.

Fig. 12

Unrooted tree of human RAS superfamily members. As with dendrograms in previous figures, branch lengths are directly proportional to the number of differences between sequences compared. Subfamilies of proteins are indicated by colored arcs: RAS (red), RHO (green), Gα (orange), ARF (yellow), and RAB (blue).

Fig. 13

Alignment of human G proteins with representative members of the RAS superfamily. The G1, G3, and G4 box motifs and surrounding sequences are presented. See Table 1 for alternate gene symbols.

Fig. 14

Dendrogram of distant G proteins (uppercase letters) with representative members of the RAS superfamily.