Structural and dynamic studies of the human RNA binding protein RBM3 reveals the molecular basis of its oligomerization and RNA recognition.

Publisher: Published by Blackwell Pub. on behalf of the Federation of European Biochemical Societies Country of Publication: England NLM ID: 101229646 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1742-4658 (Electronic) Linking ISSN: 1742464X NLM ISO Abbreviation: FEBS J Subsets: MEDLINE

Original Publication: Oxford, UK : Published by Blackwell Pub. on behalf of the Federation of European Biochemical Societies, c2005-

RNA*/metabolism ; RNA Recognition Motif* ; RNA-Binding Proteins*/metabolism; Humans ; Hydrogen Bonding ; Molecular Dynamics Simulation ; Protein Binding

Human RNA-binding motif 3 protein (RBM3) is a cold-shock protein which functions in various aspects of global protein synthesis, cell proliferation and apoptosis by interacting with the components of basal translational machinery. RBM3 plays important roles in tumour progression and cancer metastasis, and also has been shown to be involved in neuroprotection and endoplasmic reticulum stress response. Here, we have solved the solution NMR structure of the N-terminal 84 residue RNA recognition motif (RRM) of RBM3. The remaining residues are rich in RGG and YGG motifs and are disordered. The RRM domain adopts a βαββαβ topology, which is found in many RNA-binding proteins. NMR-monitored titration experiments and molecular dynamic simulations show that the beta-sheet and two loops form the RNA-binding interface. Hydrogen bond, pi-pi and pi-cation are the key interactions between the RNA and the RRM domain. NMR, size exclusion chromatography and chemical cross-linking experiments show that RBM3 forms oligomers in solution, which is favoured by decrease in temperature, thus, potentially linking it to its function as a cold-shock protein. Temperature-dependent NMR studies revealed that oligomerization of the RRM domain occurs via nonspecific interactions. Overall, this study provides the detailed structural analysis of RRM domain of RBM3, its interaction with RNA and the molecular basis of its temperature-dependent oligomerization.
(© 2021 Federation of European Biochemical Societies.)

Gerstberger S, Hafner M & Tuschl T (2014) A census of human RNA-binding proteins. Nat Rev Genet 15, 829-845.
Masuzawa T & Oyoshi T (2020) Roles of the RGG domain and RNA recognition motif of nucleolin in G-quadruplex stabilization. ACS Omega 5, 5202-5208.
Glisovic T, Bachorik JL, Yong J & Dreyfuss G (2008) RNA-binding proteins and post-transcriptional gene regulation. FEBS Lett 582, 1977-1986.
Khan F, Daniëls MA, Folkers GE, Boelens R, Saqlan Naqvi SM & van Ingen H (2014) Structural basis of nucleic acid binding by Nicotiana tabacum glycine-rich RNA-binding protein: implications for its RNA chaperone function. Nucleic Acids Res 42, 8705-8718.
Sreedharan J, Blair IP, Tripathi VB, Hu X, Vance C, Rogelj B, Ackerley S, Durnall JC, Williams KL, Buratti E et al. (2008) TDP-43 mutations in familial and sporadic amyotrophic lateral sclerosis. Science (80-) 319, 1668-1672.
Tyzack GE, Luisier R, Taha DM, Neeves J, Modic M, Mitchell JS, Meyer I, Greensmith L, Newcombe J, Ule J et al. (2019) Widespread FUS mislocalization is a molecular hallmark of amyotrophic lateral sclerosis. Brain 142, 2572-2580.
Vanderweyde T, Apicco DJ, Youmans-Kidder K, Ash PEA, Cook C, Lummertz da Rocha E, Jansen-West K, Frame AA, Citro A, Leszyk JD et al. (2016) Interaction of tau with the RNA-binding protein TIA1 regulates tau pathophysiology and toxicity. Cell Rep 15, 1455-1466.
Repici M, Hassanjani M, Maddison DC, Garção P, Cimini S, Patel B, Szegö ÉM, Straatman KR, Lilley KS, Borsello T et al. (2019) The Parkinson’s disease-linked protein DJ-1 associates with cytoplasmic mRNP granules during stress and neurodegeneration. Mol Neurobiol 56, 61-77.
Wang E, Lu SX, Pastore A, Chen X, Imig J, Chun-Wei Lee S, Hockemeyer K, Ghebrechristos YE, Yoshimi A, Inoue D et al. (2019) Targeting an RNA-binding protein network in acute myeloid leukemia. Cancer Cell 35, 369-384.e7.
Qian J, Hassanein M, Hoeksema MD, Harris BK, Zou Y, Chen H, Lu P, Eisenberg R, Wang J, Espinosa A et al. (2015) The RNA binding protein FXR1 is a new driver in the 3q26-29 amplicon and predicts poor prognosis in human cancers. Proc Natl Acad Sci USA 112, 3469-3474.
Chenette DM, Cadwallader AB, Antwine TL, Larkin LC, Wang J, Olwin BB & Schneider RJ (2016) Targeted mRNA decay by RNA binding protein AUF1 regulates adult muscle stem cell fate, promoting skeletal muscle integrity. Cell Rep 16, 1379-1390.
Julio AR & Backus KM (2021) New approaches to target RNA binding proteins. Curr Opin Chem Biol 62, 13-23.
Cléry A, Blatter M & Allain FHT (2008) RNA recognition motifs: boring? Not quite. Curr Opin Struct Biol 18, 290-298.
Thandapani P, O’Connor TR, Bailey TL & Richard S (2013) Defining the RGG/RG motif. Mol Cell 50, 613-623.
Tradewell ML, Yu Z, Tibshirani M, Boulanger M-C, Durham HD & Richard S (2012) Arginine methylation by PRMT1 regulates nuclear-cytoplasmic localization and toxicity of FUS/TLS harbouring ALS-linked mutations. Hum Mol Genet 21, 136-149.
Côté J & Richard S (2005) Tudor domains bind symmetrical dimethylated arginines. J Biol Chem 280, 28476-28483.
Ciuzan O, Hancock J, Pamfil D, Wilson I & Ladomery M (2015) The evolutionarily conserved multifunctional glycine-rich RNA-binding proteins play key roles in development and stress adaptation. Physiol Plant 153, 1-11.
Zhu X, Bührer C & Wellmann S (2016) Cold-inducible proteins CIRP and RBM3, a unique couple with activities far beyond the cold. Cell Mol Life Sci 73, 3839-3859.
Derry JMJ, Kerns JA & Francke U (1995) RBM3, a novel human gene in Xp11.23 with a putative RNA-binding domain. Hum Mol Genet 4, 2307-2311.
Danno S, Nishiyama H, Higashitsuji H, Yokoi H, Xue J-H, Itoh K, Matsuda T & Fujita J (1997) Increased transcript level of RBM3, a member of the glycine-rich RNA-binding protein family, in human cells in response to cold stress. Biochem Biophys Res Commun 236, 804-807.
Wellmann S, Bührer C, Moderegger E, Zelmer A, Kirschner R, Koehne P, Fujita J & Seeger K (2004) Oxygen-regulated expression of the RNA-binding proteins RBM3 and CIRP by a HIF-1-independent mechanism. J Cell Sci 117, 1785-1794.
Wong JJL, Au AYM, Gao D, Pinello N, Kwok C-T, Thoeng A, Lau KA, Gordon JEA, Schmitz U, Feng Y et al. (2016) RBM3 regulates temperature sensitive miR-142-5p and miR-143 (thermomiRs), which target immune genes and control fever. Nucleic Acids Res 44, 2888-2897.
Blum M, Chang H-Y, Chuguransky S, Grego T, Kandasaamy S, Mitchell A, Nuka G, Paysan-Lafosse T, Qureshi M, Raj S et al. (2021) The InterPro protein families and domains database: 20 years on. Nucleic Acids Res 49, D344-D354.
Corpet F (1988) Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res 16, 10881-10890.
Kim SS, Seffernick JT & Lindert S (2018) Accurately predicting disordered regions of proteins using rosetta ResidueDisorder application. J Phys Chem B 122, 3920-3930.
Hatos A, Hajdu-Soltész B, Monzon AM, Palopoli N, Álvarez L, Aykac-Fas B, Bassot C, Benítez GI, Bevilacqua M, Chasapi A et al. (2019) DisProt: intrinsic protein disorder annotation in 2020. Nucleic Acids Res 48, D269-D276.
Basak AJ, Maiti S, Hansda A, Mahata D, Duraivelan K, Kundapura SV, Lee W, Mukherjee G, De S & Samanta D (2020) Structural insights into N-terminal IgV domain of BTNL2, a T cell inhibitory molecule, suggests a non-canonical binding interface for its putative receptors. J Mol Biol 432, 5938-5950.
Johnson PE, Tomme P, Joshi MD & McIntosh LP (1996) Interaction of soluble cellooligosaccharides with the N-terminal cellulose-binding domain of Cellulomonas fimi CenC. 2. NMR and ultraviolet absorption spectroscopy †. Biochemistry 35, 13895-13906.
Shen Y & Bax A (2012) Identification of helix capping and β-turn motifs from NMR chemical shifts. J Biomol NMR 52, 211-232.
Ulrich EL, Akutsu H, Doreleijers JF, Harano Y, Ioannidis YE, Lin J, Livny M, Mading S, Maziuk D, Miller Z et al. (2007) BioMagResBank. Nucleic Acids Res 36, D402-D408.
Boral S, Maiti S, Basak AJ, Lee W & De S (2020) Structural, dynamic, and functional characterization of a DnaX Mini-intein derived from spirulina platensis provides important insights into intein-mediated catalysis of protein splicing. Biochemistry 59, 4711-4724.
Schubert M, Labudde D, Oschkinat H & Schmieder P (2002) A software tool for the prediction of Xaa-Pro peptide bond conformations in proteins based on 13C chemical shift statistics. J Biomol NMR 24, 149-154.
Berman H, Henrick K, Nakamura H & Markley JL (2007) The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res 35, D301-D303.
Nagai K, Oubridge C, Ito N, Avis J & Evans P (1995) The RNP domain: a sequence-specific RNA-binding domain involved in processing and transport of RNA. Trends Biochem Sci 20, 235-240.
Lu J & Hall KB (1997) Tertiary structure of RBD2 and backbone dynamics of RBD1 and RBD2 of the human U1A protein determined by NMR spectroscopy. Biochemistry 36, 10393-10405.
Garrett DS, Lodi PJ, Shamoo Y, Williams KR, Clore GM & Gronenborn AM (1994) Determination of the secondary structure and folding topology of an rna binding domain of mammalian hnRNP A1 protein using three-dimensional heteronuclear magnetic resonance spectroscopy. Biochemistry 33, 2852-2858.
Wittekind M, Gorlach M, Friedrichs M, Dreyfuss G & Mueller L (1992) 1H, 13C, and 15N NMR assignments and global folding pattern of the RNA-binding domain of the human hnRNP C proteins. Biochemistry 31, 6254-6265.
Lee AL, Kanaar R, Rio DC & Wemmer DE (1994) Resonance assignments and solution structure of the second RNA-binding domain of sex-lethal determined by multidimensional heteronuclear magnetic resonance. Biochemistry 33, 13775-13786.
Kay LE, Torchia DA & Bax A (1989) Backbone dynamics of proteins as studied by 15N inverse detected heteronuclear NMR spectroscopy: application to staphylococcal nuclease. Biochemistry 28, 8972-8979.
Halle B & Davidovic M (2003) Biomolecular hydration: from water dynamics to hydrodynamics. Proc Natl Acad Sci USA 100, 12135-12140.
Nagata T, Kanno R, Kurihara Y, Uesugi S, Imai T, Sakakibara S, Okano H & Katahira M (1999) Structure, backbone dynamics and interactions with RNA of the C-terminal RNA-binding domain of a mouse neural RNA-binding protein, Musashi1. J Mol Biol 287, 315-330.
Kneller JM, Lu M & Bracken C (2002) An effective method for the discrimination of motional anisotropy and chemical exchange. J Am Chem Soc 124, 1852-1853.
Cierpicki T & Otlewski J (2001) Amide proton temperature coefficients as hydrogen bond indicators in proteins. J Biomol NMR 21, 249-261.
De S, Greenwood AI, Rogals MJ, Kovrigin EL, Lu KP & Nicholson LK (2012) Complete thermodynamic and kinetic characterization of the isomer-specific interaction between Pin1-WW domain and the amyloid precursor protein cytoplasmic tail phosphorylated at Thr668. Biochemistry 51, 8583-8596.
van Zundert GCP, Rodrigues JPGLM, Trellet M, Schmitz C, Kastritis PL, Karaca E, Melquiond ASJ, van Dijk M, de Vries SJ & Bonvin AMJJ (2016) The HADDOCK2.2 web server: user-friendly integrative modeling of biomolecular complexes. J Mol Biol 428, 720-725.
Castello A, Fischer B, Frese CK, Horos R, Alleaume A-M, Foehr S, Curk T, Krijgsveld J & Hentze MW (2016) Comprehensive identification of RNA-binding domains in human cells. Mol Cell 63, 696-710.
Chong PA, Vernon RM & Forman-Kay JD (2018) RGG/RG motif regions in RNA binding and phase separation. J Mol Biol 430, 4650-4665.
Choi J-M, Holehouse AS & Pappu RV (2020) Physical principles underlying the complex biology of intracellular phase transitions. Annu Rev Biophys 49, 107-133.
Chappell SA, Owens GC & Mauro VP (2001) A 5′ leader of Rbm3, a cold stress-induced mRNA, mediates internal initiation of translation with increased efficiency under conditions of mild hypothermia. J Biol Chem 276, 36917-36922.
Dresios J, Aschrafi A, Owens GC, Vanderklish PW, Edelman GM & Mauro VP (2005) Cold stress-induced protein Rbm3 binds 60S ribosomal subunits, alters microRNA levels, and enhances global protein synthesis. Proc Natl Acad Sci USA 102, 1865-1870.
Zhu X, Zelmer A, Kapfhammer JP & Wellmann S (2016) Cold-inducible RBM3 inhibits PERK phosphorylation through cooperation with NF90 to protect cells from endoplasmic reticulum stress. FASEB J 30, 624-634.
Si W, Li Z, Huang Z, Ye S, Li X, Li Y, Kuang W, Chen D & Zhu M (2020) RNA binding protein motif 3 inhibits oxygen-glucose deprivation/reoxygenation-induced apoptosis through promoting stress granules formation in PC12 cells and rat primary cortical neurons. Front Cell Neurosci 14, 1-14.
Schneider CA, Rasband WS & Eliceiri KW (2012) NIH Image to ImageJ: 25 years of image analysis. Nat Methods 9, 671-675.
Sattler M (1999) Heteronuclear multidimensional NMR experiments for the structure determination of proteins in solution employing pulsed field gradients. Prog Nucl Magn Reson Spectrosc 34, 93-158.
Delaglio F, Grzesiek S, Vuister G, Zhu G, Pfeifer J & Bax A (1995) NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 6, 277-293.
Lee W, Tonelli M & Markley JL (2015) NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy. Bioinformatics 31, 1325-1327.
Lee W, Bahrami A, Dashti HT, Eghbalnia HR, Tonelli M, Westler WM & Markley JL (2019) I-PINE web server: an integrative probabilistic NMR assignment system for proteins. J Biomol NMR 73, 213-222.
Lee W, Petit CM, Cornilescu G, Stark JL & Markley JL (2016) The AUDANA algorithm for automated protein 3D structure determination from NMR NOE data. J Biomol NMR 65, 51-57.
Lee W, Stark JL & Markley JL (2014) PONDEROSA-C/S: client-server based software package for automated protein 3D structure determination. J Biomol NMR 60, 73-75.
Schwieters CD, Kuszewski JJ, Tjandra N & Marius Clore G (2003) The Xplor-NIH NMR molecular structure determination package. J Magn Reson 160, 65-73.
Lee W, Rahimi M, Lee Y & Chiu A (2021) POKY: a software suite for multidimensional NMR and 3D structure calculation of biomolecules. Bioinformatics 37, 3041-3042.
Bhattacharya A, Tejero R & Montelione GT (2007) Evaluating protein structures determined by structural genomics consortia. Proteins 66, 778-795.
Kabsch W & Sander C (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22, 2577-2637.
Trainor K, Palumbo JA, MacKenzie DWS & Meiering EM (2020) Temperature dependence of NMR chemical shifts: tracking and statistical analysis. Protein Sci 29, 306-314.
Maiti S, Acharya B, Boorla VS, Manna B, Ghosh A & De S (2019) Dynamic studies on intrinsically disordered regions of two paralogous transcription factors reveal rigid segments with important biological functions. J Mol Biol 431, 1353-1369.
Dosset P, Hus JC, Blackledge M & Marion D (2000) Efficient analysis of macromolecular rotational diffusion from heteronuclear relaxation data. J Biomol NMR 16, 23-28.
Handa N, Nureki O, Kurimoto K, Kim I, Sakamoto H, Shimura Y, Muto Y & Yokoyama S (1999) Structural basis for recognition of the tra mRNA precursor by the Sex-lethal protein. Nature 398, 579-585.
Van Der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE & Berendsen HJC (2005) GROMACS: fast, flexible, and free. J Comput Chem 26, 1701-1718.
Hornak V, Abel R, Okur A, Strockbine B, Roitberg A & Simmerling C (2006) Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins 65, 712-725.
Darden T, York D & Pedersen L (1993) Particle mesh Ewald: an N ⋅log( N ) method for Ewald sums in large systems. J Chem Phys 98, 10089-10092.
Hess B (2008) P-LINCS: a parallel linear constraint solver for molecular simulation. J Chem Theory Comput 4, 116-122.
Bussi G, Donadio D & Parrinello M (2007) Canonical sampling through velocity rescaling. J Chem Phys 126, 014101.
Parrinello M & Rahman A (1981) Polymorphic transitions in single crystals: a new molecular dynamics method. J Appl Phys 52, 7182-7190.
Kirchner DK & Güntert P (2011) Objective identification of residue ranges for the superposition of protein structures. BMC Bioinformatics 12, 170.
The PyMOL molecular graphics system, Version 2.4.1. Schrödinger, LLC, New York, NY.

Keywords: NMR relaxation; RRM domain; cold-shock protein; molecular dynamics simulation; protein-RNA interaction

0 (RBM3 protein, human)
0 (RNA-Binding Proteins)
63231-63-0 (RNA)

Date Created: 20211127 Date Completed: 20220519 Latest Revision: 20220615

20240829

10.1111/febs.16301

34837346