κB-Ras proteins are fast-exchanging GTPases and function via nucleotide-independent binding of Ral GTPase-activating protein complexes.
GTP hydrolysis by small GTPases
RalGAP
cancer mutations
nucleotide binding of small GTPases
κB‐Ras
Journal
FEBS letters
ISSN: 1873-3468
Titre abrégé: FEBS Lett
Pays: England
ID NLM: 0155157
Informations de publication
Date de publication:
11 Apr 2024
11 Apr 2024
Historique:
revised:
29
01
2024
received:
26
09
2023
accepted:
27
02
2024
medline:
12
4
2024
pubmed:
12
4
2024
entrez:
11
4
2024
Statut:
aheadofprint
Résumé
κB-Ras (NF-κB inhibitor-interacting Ras-like protein) GTPases are small Ras-like GTPases but harbor interesting differences in important sequence motifs. They act in a tumor-suppressive manner as negative regulators of Ral (Ras-like) GTPase and NF-κB signaling, but little is known about their mode of function. Here, we demonstrate that, in contrast to predictions based on primary structure, κB-Ras GTPases possess hydrolytic activity. Combined with low nucleotide affinity, this renders them fast-cycling GTPases that are predominantly GTP-bound in cells. We characterize the impact of κB-Ras mutations occurring in tumors and demonstrate that nucleotide binding affects κB-Ras stability but is not strictly required for RalGAP (Ral GTPase-activating protein) binding. This demonstrates that κB-Ras control of RalGAP/Ral signaling occurs in a nucleotide-binding- and switch-independent fashion.
Identifiants
pubmed: 38604989
doi: 10.1002/1873-3468.14860
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : Deutsche Forschungsgemeinschaft
ID : KU2531/6-1
Organisme : Deutsche Forschungsgemeinschaft
ID : OE531/3-3
Organisme : Deutsche Forschungsgemeinschaft
ID : OE531/4-1
Informations de copyright
© 2024 The Authors. FEBS Letters published by John Wiley & Sons Ltd on behalf of Federation of European Biochemical Societies.
Références
Wennerberg K, Rossman KL and Der CJ (2005) The Ras superfamily at a glance. J Cell Sci 118, 843–846.
Cox AD and Der CJ (2010) Ras history: the saga continues. Small GTPases 1, 2–27.
Vetter IR and Wittinghofer A (2001) The guanine nucleotide‐binding switch in three dimensions. Science 294, 1299–1304.
Bos JL, Rehmann H and Wittinghofer A (2007) GEFs and GAPs: critical elements in the control of small G proteins. Cell 129, 865–877.
Cherfils J and Zeghouf M (2013) Regulation of small GTPases by GEFs, GAPs, and GDIs. Physiol Rev 93, 269–309.
Bourne HR, Sanders DA and McCormick F (1991) The GTPase superfamily: conserved structure and molecular mechanism. Nature 349, 117–127.
Paduch M, Jeleń F and Otlewski J (2001) Structure of small G proteins and their regulators. Acta Biochim Pol 48, 829–850.
Vetter IR (2014) The structure of the G domain of the Ras superfamily. In Ras Superfamily Small G Proteins: Biology and Mechanisms 1 (Wittinghofer A, ed.), pp. 25–50. Springer, Vienna.
Wittinghofer A and Vetter IR (2011) Structure‐function relationships of the G domain, a canonical switch motif. Annu Rev Biochem 80, 943–971.
Fenwick C, Na SY, Voll RE, Zhong H, Im SY, Lee JW and Ghosh S (2000) A subclass of Ras proteins that regulate the degradation of IkappaB. Science 287, 869–873.
Oeckinghaus A and Ghosh S (2009) The NF‐kappaB family of transcription factors and its regulation. Cold Spring Harb Perspect Biol 1, a000034.
Hayden MS and Ghosh S (2008) Shared principles in NF‐kappaB signaling. Cell 132, 344–362.
Chen Y, Wu J and Ghosh G (2003) KappaB‐Ras binds to the unique insert within the ankyrin repeat domain of IkappaBbeta and regulates cytoplasmic retention of IkappaBbeta x NF‐kappaB complexes. J Biol Chem 278, 23101–23106.
Chen Y, Vallee S, Wu J, Vu D, Sondek J and Ghosh G (2004) Inhibition of NF‐kappaB activity by IkappaBbeta in association with kappaB‐Ras. Mol Cell Biol 24, 3048–3056.
Tago K, Funakoshi‐Tago M, Sakinawa M, Mizuno N and Itoh H (2010) KappaB‐Ras is a nuclear‐cytoplasmic small GTPase that inhibits NF‐kappaB activation through the suppression of transcriptional activation of p65/RelA. J Biol Chem 285, 30622–30633.
Oeckinghaus A, Postler TS, Rao P, Schmitt H, Schmitt V, Grinberg‐Bleyer Y, Kühn LI, Gruber CW, Lienhard GE and Ghosh S (2014) κB‐Ras proteins regulate both NF‐κB‐dependent inflammation and Ral‐dependent proliferation. Cell Rep 8, 1793–1807.
Postler TS and Ghosh S (2015) Bridging the gap: a regulator of NF‐κB linking inflammation and cancer. J Oral Biosci 57, 143–147.
Sarais F, Rebl H, Verleih M, Ostermann S, Krasnov A, Köllner B, Goldammer T and Rebl A (2020) Characterisation of the teleostean κB‐Ras family: the two members NKIRAS1 and NKIRAS2 from rainbow trout influence the activity of NF‐κB in opposite ways. Fish Shellfish Immunol 106, 1004–1013.
Chen X‐W, Leto D, Xiong T, Yu G, Cheng A, Decker S and Saltiel AR (2011) A Ral GAP complex links PI 3‐kinase/Akt signaling to RalA activation in insulin action. Mol Biol Cell 22, 141–152.
Gridley S, Lane WS, Garner CW and Lienhard GE (2005) Novel insulin‐elicited phosphoproteins in adipocytes. Cell Signal 17, 59–66.
Gridley S, Chavez JA, Lane WS and Lienhard GE (2006) Adipocytes contain a novel complex similar to the tuberous sclerosis complex. Cell Signal 18, 1626–1632.
Shirakawa R, Fukai S, Kawato M, Higashi T, Kondo H, Ikeda T, Nakayama E, Okawa K, Nureki O, Kimura T et al. (2009) Tuberous sclerosis tumor suppressor complex‐like complexes act as GTPase‐activating proteins for Ral GTPases. J Biol Chem 284, 21580–21588.
Wong CH, Li YJ and Chen YC (2016) Therapeutic potential of targeting acinar cell reprogramming in pancreatic cancer. World J Gastroenterol 22, 7046–7057.
Postler TS, Wang A, Brundu FG, Wang P, Wu Z, Butler KE, Grinberg‐Bleyer Y, Krishnareddy S, Lagana SM, Saqi A et al. (2023) A pan‐cancer analysis implicates human NKIRAS1 as a tumor‐suppressor gene. Proc Natl Acad Sci USA 120, e2312595120.
Beel S, Kolloch L, Apken LH, Jürgens L, Bolle A, Sudhof N, Ghosh S, Wardelmann E, Meisterernst M, Steinestel K et al. (2020) κB‐Ras and Ral GTPases regulate acinar to ductal metaplasia during pancreatic adenocarcinoma development and pancreatitis. Nat Commun 11, 3409.
Jumper J, Evans R, Pritzel A, Green T, Figurnov M, Ronneberger O, Tunyasuvunakool K, Bates R, Žídek A, Potapenko A et al. (2021) Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589.
Pai EF, Krengel U, Petsko GA, Goody RS, Kabsch W and Wittinghofer A (1990) Refined crystal structure of the triphosphate conformation of H‐ras p21 at 1.35 A resolution: implications for the mechanism of GTP hydrolysis. EMBO J 9, 2351–2359.
Niesen FH, Berglund H and Vedadi M (2007) The use of differential scanning fluorimetry to detect ligand interactions that promote protein stability. Nat Protoc 2, 2212–2221.
Klostermeier D and Rudolph MG (2017) Biophysical Chemistry. CRC Press, Boca Raton, FL.
Eberth A and Ahmadian MR (2009) In vitro GEF and GAP assays. Curr Protoc Cell Biol 43, 14.9.1–14.9.25.
Mondal S, Hsiao K and Goueli SA (2015) A homogenous bioluminescent system for measuring GTPase, GTPase activating protein, and guanine nucleotide exchange factor activities. Assay Drug Dev Technol 13, 444–455.
Hekkelman ML, de Vries I, Joosten RP and Perrakis A (2023) AlphaFill: enriching AlphaFold models with ligands and cofactors. Nat Methods 20, 205–213.
Scrima A, Thomas C, Deaconescu D and Wittinghofer A (2008) The Rap‐RapGAP complex: GTP hydrolysis without catalytic glutamine and arginine residues. EMBO J 27, 1145–1153.
John J, Sohmen R, Feuerstein J, Linke R, Wittinghofer A and Goody RS (1990) Kinetics of interaction of nucleotides with nucleotide‐free H‐ras p21. Biochemistry 29, 6058–6065.
Cerami E, Gao J, Dogrusoz U, Gross BE, Sumer SO, Aksoy BA, Jacobsen A, Byrne CJ, Heuer ML, Larsson E et al. (2012) The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov 2, 401–404.
Gao J, Aksoy BA, Dogrusoz U, Dresdner G, Gross B, Sumer SO, Sun Y, Jacobsen A, Sinha R, Larsson E et al. (2013) Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci Signal 6, pl1.
de Bruijn I, Kundra R, Mastrogiacomo B, Tran TN, Sikina L, Mazor T, Li X, Ochoa A, Zhao G, Lai B et al. (2023) Analysis and visualization of longitudinal genomic and clinical data from the AACR Project GENIE biopharma collaborative in cBioPortal. Cancer Res 83, 3861–3867.
Apken LH and Oeckinghaus A (2020) The RAL signaling network: cancer and beyond. Int Rev Cell Mol Biol 361, 21–105.
Gasper R and Wittinghofer F (2019) The Ras switch in structural and historical perspective. Biol Chem 401, 143–163.
Calixto AR, Moreira C, Pabis A, Kötting C, Gerwert K, Rudack T and Kamerlin SCL (2019) GTP hydrolysis without an active site base: a unifying mechanism for Ras and related GTPases. J Am Chem Soc 141, 10684–10701.
Rudack T, Xia F, Schlitter J, Kötting C and Gerwert K (2012) The role of magnesium for geometry and charge in GTP hydrolysis, revealed by quantum mechanics/molecular mechanics simulations. Biophys J 103, 293–302.
Neal SE, Eccleston JF, Hall A and Webb MR (1988) Kinetic analysis of the hydrolysis of GTP by p21N‐ras. The basal GTPase mechanism. J Biol Chem 263, 19718–19722.
Reinstein J, Schlichting I, Frech M, Goody RS and Wittinghofer A (1991) p21 with a phenylalanine 28 → leucine mutation reacts normally with the GTPase activating protein GAP but nevertheless has transforming properties. J Biol Chem 266, 17700–17706.
Praefcke GJK and McMahon HT (2004) The dynamin superfamily: universal membrane tubulation and fission molecules? Nat Rev Mol Cell Biol 5, 133–147.
Kanie T, Abbott KL, Mooney NA, Plowey ED, Demeter J and Jackson PK (2017) The CEP19‐RABL2 GTPase complex binds IFT‐B to initiate intraflagellar transport at the ciliary base. Dev Cell 42, 22–36.e12.
Ivanova AA, Caspary T, Seyfried NT, Duong DM, West AB, Liu Z and Kahn RA (2017) Biochemical characterization of purified mammalian ARL13B protein indicates that it is an atypical GTPase and ARL3 guanine nucleotide exchange factor (GEF). J Biol Chem 292, 11091–11108.
Bhogaraju S, Taschner M, Morawetz M, Basquin C and Lorentzen E (2011) Crystal structure of the intraflagellar transport complex 25/27. EMBO J 30, 1907–1918.
Braga V (2018) Signaling by small GTPases at cell‐cell junctions: protein interactions building control and networks. Cold Spring Harb Perspect Biol 10, a028746.
Nola S, Daigaku R, Smolarczyk K, Carstens M, Martin‐Martin B, Longmore G, Bailly M and Braga VMM (2011) Ajuba is required for Rac activation and maintenance of E‐cadherin adhesion. J Cell Biol 195, 855–871.
Lam BD and Hordijk PL (2013) The Rac1 hypervariable region in targeting and signaling: a tail of many stories. Small GTPases 4, 78–89.
Reyes CC, Jin M, Breznau EB, Espino R, Delgado‐Gonzalo R, Goryachev AB and Miller AL (2014) Anillin regulates cell‐cell junction integrity by organizing junctional accumulation of Rho‐GTP and actomyosin. Curr Biol 24, 1263–1270.
Feig LA and Cooper GM (1988) Inhibition of NIH 3T3 cell proliferation by a mutant ras protein with preferential affinity for GDP. Mol Cell Biol 8, 3235–3243.
Feig LA (1999) Tools of the trade: use of dominant‐inhibitory mutants of Ras‐family GTPases. Nat Cell Biol 1, E25–E27.
Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J et al. (2011) Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 7, 539.