The Mystery of Rap1 Suppression of Oncogenic Ras - PubMed (original) (raw)

Review

The Mystery of Rap1 Suppression of Oncogenic Ras

Ruth Nussinov et al. Trends Cancer. 2020 May.

Abstract

Decades ago, Rap1, a small GTPase very similar to Ras, was observed to suppress oncogenic Ras phenotype, reverting its transformation. The proposed reason, persisting since, has been competition between Ras and Rap1 for a common target. Yet, none was found. There was also Rap1's puzzling suppression of Raf-1 versus activation of BRAF. Reemerging interest in Rap1 envisages capturing its Ras suppression action by inhibitors. Here, we review the literature and resolve the enigma. In vivo oncogenic Ras exists in isoform-distinct nanoclusters. The presence of Rap1 within the nanoclusters reduces the number of the clustered oncogenic Ras molecules, thus suppressing Raf-1 activation and mitogen-activated protein kinase (MAPK) signaling. Nanoclustering suggests that Rap1 suppression is Ras isoform dependent. Altogether, a potent Rap1-like inhibitor appears unlikely.

Keywords: BRAF; K-RAS; K-Ras dimers; KRAS; KRAS4A; KRAS4B; NORE1A; Raf; Raf-1; cancer; drug discovery; inhibitors; nanocluster; signaling pathways.

PubMed Disclaimer

Figures

Figure 1.

Oncogenic Ras forms nanoclusters and promotes Raf dimerization, activation, and signaling in the mitogen-activated protein kinase (MAPK) pathway (Raf/MEK/ERK). In the cytosol, Raf is autoinhibited, but the high-affinity Ras–(RBD) Ras-binding domain interaction releases the autoinhibition. Raf is activated through side-by-side dimerization. Rap1 dilutes oncogenic Ras nanoclusters, suppressing Raf’s activation. Abbreviations: CRD, cysteine-rich domain; KD, kinase domain.

Figure 2.. Comparison between BRAF and Raf-1.

(A) Sequences of conserved region (CR)1 and (B) domain structures of BRAF and Raf-1. In the sequence, hydrophobic, polar/glycine, positively charged, and negatively charged residues are colored black, green, blue, and red, respectively. Gray denotes the unstructured loop region. All Raf kinases share three conserved regions; CR1 involves the Ras-binding domain (RBD) and cysteine-rich domain (CRD), CR2 contains the Ser/Thr-rich region at the flexible linker, and CR3 is the kinase domain. (C) Crystal structures of BRAF RBD (PDB: 3NY5) and Raf-1 RBD (PDB: 4G0N), and solution structure of Raf-1 CRD (PDB: 1FAR). (D) Crystal structures of the kinase domain homodimer for BRAF (PDB: 6U2H) and (E) Raf-1 (PDB: 3OMV). Raf domain structures are highly homologous among the isoforms.

Figure 3.. Decreased Rap1 Expression is Associated with KRas Mutation.

(A) Shallow deletion of RAP1A and KRAS mutation co-occur in pancreatic and lung cancers. The distribution of KRAS somatic mutations and RAP1A copy number variations (CNV) in the Cancer Genome Atlas (TCGA) pancreatic and lung cancers obtained from cBioPortal. cBioPortal was queried over all completed tumors from the PanCancer Atlas datasets using the Onco Query Language (OQL), ‘RAP1A:HETLOSS; KRAS: G12, G13, K61.’ (B) Shallow deletion of RAP1A leads to decreased mRNA in pancreatic and lung cancers. The plots are generated by cBioPortal (

www.cbioportal.org

) [97,98]. Abbreviation: GISTIC, Genomic Identification of Significant Targets in Cancer.

Figure 4.. Comparison between Rap1 and Ras.

(A) Sequence similarity among Ras family, including Rap1, KRas4B, and HRas. In the sequence, hydrophobic, polar/glycine, positively charged, and negatively charged residues are colored black, green, blue, and red, respectively. (B) Model structures of KRas4B catalytic domain interacting with BRAF Ras-binding domain (RBD) (upper left) and Raf-1 RBD (upper right), based on our previous studies [87]. In addition to the strong β-sheet interaction, Ras adds stability to the interaction with the RBDs through the salt bridges between E31 and K183 for BRAF, and between E31 and K84/K87 for Raf-1. Rap1 can interact with BRAF RBD due to distant repulsive force between K31 and K183 (lower left). However, in the interaction with Raf-1 RBD, Rap1 K31 electrostatically crashes with K84/K87, leading to dissociation. (C) Model structures of Rap1 interacting with Raf-1 conserved region (CR)1 (left) and BRAF CR1 at the anionic membrane. Rap1 prefers to bind Raf-1 cysteine-rich domain (CRD), while it binds to BRAF RBD. (D) Schematic diagram of Raf activation by Rap1. Abbreviations: KD, kinase domain; HVR, hypervariable region.

References

1. Kitayama H et al. (1989) A ras-related gene with transformation suppressor activity. Cell 56, 77–84 - PubMed
1. Cook SJ et al. (1993) RapV12 antagonizes Ras-dependent activation of ERK1 and ERK2 by LPA and EGF in Rat-1 fibro-blasts. EMBO J. 12, 3475–3485 - PMC - PubMed
1. Sprang SR (1995) How Ras works: structure of a Rap–Raf complex. Structure 3, 641–643 - PubMed
1. Zwartkruis FJ and Bos JL (1999) Ras and Rap1: two highly related small GTPases with distinct function. Exp. Cell Res 253, 157–165 - PubMed
1. Shah S et al. (2019) Ras and Rap1: a tale of two GTPases. Semin. Cancer Biol 54, 29–39 - PMC - PubMed

The Mystery of Rap1 Suppression of Oncogenic Ras - PubMed (original) (raw)