RASEF

Ras and EF-hand domain-containing protein also known as Ras-related protein Rab-45 is a protein that in humans is encoded by the RASEF gene.^[5]

RASEF
Available structures PDB Ortholog search: PDBe RCSB List of PDB id codes 2P5S, 2PMY
Identifiers
Aliases	RASEF, RAB45, RAS and EF-hand domain containing, TSG
External IDs	OMIM: 611344 MGI: 2448565 HomoloGene: 28424 GeneCards: RASEF
Gene location (Human) Chr. Chromosome 9 (human)^[1] Band 9q21.32 Start 82,979,590 bp^[1] End 83,063,177 bp^[1]
Gene location (Mouse) Chr. Chromosome 4 (mouse)^[2] Band 4|4 C3 Start 73,632,816 bp^[2] End 73,709,231 bp^[2]
RNA expression pattern Bgee Human Mouse (ortholog) Top expressed in pancreatic epithelial cell sperm pancreatic ductal cell caput epididymis secondary oocyte bronchial epithelial cell body of pancreas trachea palpebral conjunctiva amniotic fluid Top expressed in epithelium of stomach left colon parotid gland conjunctival fornix spermatid Paneth cell seminal vesicula lacrimal gland vestibular labyrinth olfactory epithelium More reference expression data BioGPS n/a
Gene ontology Molecular function nucleotide binding calcium ion binding metal ion binding GTPase activity GTP binding GDP binding identical protein binding Cellular component cytoplasm cytosol perinuclear region of cytoplasm Biological process protein homooligomerization Sources:Amigo / QuickGO
Orthologs Species Human Mouse Entrez 158158 242505 Ensembl ENSG00000165105 ENSMUSG00000043003 UniProt Q8IZ41 Q5RI75 RefSeq (mRNA) NM_152573 NM_001017427 RefSeq (protein) NP_689786 NP_001017427 NP_001391890 NP_001391891 NP_001391892 Location (UCSC) Chr 9: 82.98 – 83.06 Mb Chr 4: 73.63 – 73.71 Mb PubMed search ^[3] ^[4]
Wikidata
View/Edit Human View/Edit Mouse

The RASEF gene is located on chromosome 9 (9q21.32).^[6]

Introduction

RASEF belongs to the small GTPase family, which means that it's able to hydrolyse a molecule of GTP; known for its unusual conformation. In the small GTPase family it is classified in the RAS domain, a special group of oncogenes and oncoproteins that take part in the synthesis of molecules related to cell reproduction.^[7]

A feature of RASEF is its N-terminal EF-hand motif and C-terminal Rab-homology domain, that enables it to bind calcium.^[7] Lately, RASEF has been studied for its role as an oncoprotein. Investigating which mutations affect it and how we could inhibit them could allow us to fight cancers that have an elevated mortality rate, such as lung cancer.^[7]

Oncogenes

When studying cancer's molecular biology we can identify two types of genes that intervene in its development:

• Tumor suppressor genes: Inhibit tumor formation.
• Oncogenes: Stimulate cell proliferation. It is in this group where members of the RAS family are found.

Oncogenes generally code for growth factors and their receptors, enzymes related to transduction signal or for DNA transcription factors. When those genes suffer some kind of mutation or translocation, they can change their conformation and cause a catalytic activity in cell reproduction that is normally inactivated, which causes abnormal cell proliferation. This could provoke a malignant tumor if combined with a separate mutation in a protein's RAS group.^[8]

Ras / Rab family

RASEF or Rab 45 is classified in the Ras superfamily, which includes small (20kDa) guanosine triphosphatases (GTPases). The basic members of this group of proteins are Ras oncogenes. It's divided into five major families (Ras, Rho, Arf/Sar, Ran and Rab).^[9] RASEF is included in the Rab family (the largest family), which is responsible for vesicular traffic of proteins between organelles via endocytotic and secretory pathways. Their function is to make budding from the donor compartment, transport, vesicle fusion and cargo release easier.^[10]

Structure

RASEF is a 740 amino acids^[11] long protein which contains 3 distinct regions: 2 EF hand domains (which in turn contain 2 Calcium bindings and 3 nucleotide bindings -assumed by similarity with other proteins, without direct evidence-), a Coiled Coil region and a C-terminal Rab-homology domain.^[7]

Domains

N-terminal EF hand domain

Sequence found in RASEF protein that contains 35 amino acids (36 in the second one). The two EF hand domains are consecutively located at the “beginning” of the protein. Its name “N-terminal” indicates an amino group (characteristic of this group of biomolecules, as well as the C- terminal ending). The first one goes from the 8th amino acid to the 42nd, and the other to the 42nd to the 77th.^[9] “EF hand” refers to the shape of this domain (similarity with the right hand's morphology). Ca+2 ions are responsible for this structure, which by binding metals join two alpha helixes.^[12]

Coiled coil region

Structural motif in proteins: from two to seven alpha helixes entwined. Each one of these helixes is a repeated 7 amino acid sequence (HPPHCPC), where H refers to hydrophobic amino acids.^[13] The position of hydrophobic remains (alpha helix exterior) causes their amphipathic behaviour.^{[citation needed]} The bond between different chains, produced in cytoplasm (aqueous region), is extremely tight, as Van der Waals forces appear between the hydrophobic radicals (H), surrounded by the hydrophilic amino acids (amphipathic molecule). This bond is known as the “Knobs into holes packing”.^[14]Coiled coil motif, located in the intermediate region of the protein, is responsible for self-interaction.^[15]

C-Terminal Rab-homology domain

Located at the end of the protein (opposite to N-terminal domain), it's a carboxyl group (COOH). In this region, there are guanine nucleotide bonds to tri-phosphates and di-phosphates. The variability of this domain is responsible for the high appearance of elements needed in the joints between proteins and their targets in the membrane.^[16] Both the C-Terminal Rab-homology domain and the intermediate region of the protein are responsible for the intracellular location of the protein (perinuclear region).^{[citation needed]}

Function

RASEF intervenes in a direct manner in biological processes such as protein transport and small GTPase mediated signal transduction. Its molecular functions include GTP binding and calcium ion binding.^[17]

As mentioned previously, RASEF has 3 distinct structural regions: the C-terminus Rab domain, the N-terminus EF-hand domain and the self-interacting mid-region. Each of these has an individual function.^{[citation needed]}

The guanine-nucleotide forms of the Rab domain regulate the protein's localization. RASEF is mainly found in the perinuclear region of the cell. In addition, the protein's mid-region also seems to be involved in the perinuclear localization. This could be due to its interaction with membrane compartments.^{[citation needed]} The EF-hand domain's function still remains to be discovered. However, it is speculated that due to its conformational changes upon binding with Ca2+ ions, and these being responsible for interactions with target molecules; that in cooperation with the Rab-domain, the EF-hand domain's main function is regulating membrane traffic.^{[citation needed]} Over 60 Rab-family GTPase proteins have key roles in membrane traffic regulation. This isn't surprising given the amount and variety of intracellular compartments, which require a high level of control to ensure a proper delivery and fusion of vesicles at the correct site.^[7]

This connects the RASEF protein directly to cell-growth mechanisms, making it susceptible to having a decisive role in the apparition of cancerous cells.^{[citation needed]}

Clinical significance

Ras and Ef-hand domain containing proteins are commonly overexpressed in primary lung cancers and its intervention is crucial for the proliferation and survival of cancerous cells. Apart from binding calcium ions in the N-terminus, RASEF plays a significant role in lung cancer cell-growth. This occurs because of its interaction with ERK (extracellular signal-regulated kinase) molecules involved in the regulation of meiosis, mitosis, and postmitotic functions in differentiated cells, whose pathway can be activated by carcinogens or viral infections. .^[18]

There is ongoing research that is studying the possibility of using RASEF as a clinically promising prognostic biomarker and therapeutic target for lung cancer. Some recent studies have revealed the viability of using RASEF as a target for this disease.^[18]

Also, a segregation study in families with uveal and cutaneous melanoma identified a potential locus harboring a tumor-suppressor gene (TSG). One of the genes in this area (9q21), RASEF, was then analyzed as a candidate TSG, but the lack of point mutations and copy number changes could not confirm this. Nowadays, the RASEF gene has been investigated for potential mutations and gene silencing by promoting methylation in uveal melanoma. It appears to be the mechanism targeting RASEF in uveal melanoma, and allelic imbalance at this locus supports a TSG role for the Ras and Ef-hand domain containing.^[19]

References

1. GRCh38: Ensembl release 89: ENSG00000165105 - Ensembl, May 2017
2. GRCm38: Ensembl release 89: ENSMUSG00000043003 - Ensembl, May 2017
3. "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
4. "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
5. "Entrez Gene: RAS and EF-hand domain containing".
6. Sweetser DA, Peniket AJ, Haaland C, Blomberg AA, Zhang Y, Zaidi ST, Dayyani F, Zhao Z, Heerema NA, Boultwood J, Dewald GW, Paietta E, Slovak ML, Willman CL, Wainscoat JS, Bernstein ID, Daly SB (November 2005). "Delineation of the minimal commonly deleted segment and identification of candidate tumor-suppressor genes in del(9q) acute myeloid leukemia". Genes Chromosomes Cancer. 44 (3): 279–91. doi:10.1002/gcc.20236. PMID 16015647. S2CID 25536746.
7. Shintani M, Tada M, Kobayashi T, Kajiho H, Kontani K, Katada T (June 2007). "Characterization of Rab45/RASEF containing EF-hand domain and a coiled-coil motif as a self-associating GTPase". Biochem. Biophys. Res. Commun. 357 (3): 661–7. doi:10.1016/j.bbrc.2007.03.206. PMID 17448446.
8. Burtis CA, Bruns DE (2015). "Tumor Markers and Cancer Genes". Tietz Fundamentals of Clinical Chemistry and Molecular Diagnostics (Seventh ed.). St. Louis: Elsevier Health Sciences. p. 359. ISBN 978-0-323-29206-1.
9. Mulloy JC, Cancelas JA, Filippi MD, Kalfa TA, Guo F, Zheng Y (February 2010). "Rho GTPases in hematopoiesis and hemopathies". Blood. 115 (5): 936–47. doi:10.1182/blood-2009-09-198127. PMC 2817638. PMID 19965643.
10. Rojas AM, Fuentes G, Rausell A, Valencia A (January 2012). "The Ras protein superfamily: evolutionary tree and role of conserved amino acids". J. Cell Biol. 196 (2): 189–201. doi:10.1083/jcb.201103008. PMC 3265948. PMID 22270915.
11. "RCSB PDB - Protein Feature View - Ras and EF-hand domain-containing protein - Q8IZ41 (RASEF_HUMAN)".
12. Branden C, Tooze J (1999). "Chapter 2: Motifs of protein structure". Introduction to Protein Structure. New York: Garland Pub. pp. 24–25. ISBN 0-8153-2305-0.
13. Mason JM, Arndt KM (February 2004). "Coiled coil domains: stability, specificity, and biological implications". ChemBioChem. 5 (2): 170–6. doi:10.1002/cbic.200300781. PMID 14760737. S2CID 39252601.
14. Crick FH (November 1952). "Is alpha-keratin a coiled coil?". Nature. 170 (4334): 882–3. Bibcode:1952Natur.170..882C. doi:10.1038/170882b0. PMID 13013241. S2CID 4147931.
15. Burkhard P, Stetefeld J, Strelkov SV (February 2001). "Coiled coils: a highly versatile protein folding motif". Trends Cell Biol. 11 (2): 82–8. doi:10.1016/S0962-8924(00)01898-5. PMID 11166216.
16. Chavrier P, Gorvel JP, Stelzer E, Simons K, Gruenberg J, Zerial M (October 1991). "Hypervariable C-terminal domain of rab proteins acts as a targeting signal". Nature. 353 (6346): 769–72. Bibcode:1991Natur.353..769C. doi:10.1038/353769a0. PMID 1944536. S2CID 1641331.
17. "Gene: RASEF". Ensembl Project. Cambridge, United Kingdom: European Molecular Biology Laboratory's European Bioinformatics Institute. ENSG00000165105.
18. Oshita H, Nishino R, Takano A, Fujitomo T, Aragaki M, Kato T, Akiyama H, Tsuchiya E, Kohno N, Nakamura Y, Daigo Y (August 2013). "RASEF is a novel diagnostic biomarker and a therapeutic target for lung cancer". Mol. Cancer Res. 11 (8): 937–51. doi:10.1158/1541-7786.MCR-12-0685-T. PMID 23686708.
19. Maat W, Beiboer SH, Jager MJ, Luyten GP, Gruis NA, van der Velden PA (April 2008). "Epigenetic regulation identifies RASEF as a tumor-suppressor gene in uveal melanoma". Invest. Ophthalmol. Vis. Sci. 49 (4): 1291–8. doi:10.1167/iovs.07-1135. PMID 18385040.